Biochemical and Cellular Properties of ATP7B Variants

Chapter 4

Biochemical and Cellular Properties of ATP7B Variants Samuel Jayakanthan, Courtney McCann and Svetlana Lutsenko Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, United States

INTRODUCTION Cells employ copper (Cu) to activate oxygen and facilitate electron-transfer reactions. The ability of copper (Cu) to readily cycle between the Cu(I) and Cu(II) oxidation states makes this metal an indispensable cofactor for a variety of enzymes that are critical for organism function and survival. These enzymes participate in such processes as respiration, defense against oxygen radicals, biosynthesis of neuromodulators, iron transport, and other important processes [1, 2]. However, under conditions of Cu overload, observed in Wilson disease, redox properties of Cu became detrimental to cells causing metabolic abnormalities, inflammation, and cell death [3]. To maintain Cu homeostasis, human cells utilize the high-affinity Cu transporter CTR1 (for Cu uptake) and two Cu-transporting ATPases (Cu-ATPases) ATP7A and ATP7B (for Cu export) [4, 5]. These Cu transporters work together with Atox1, a small cytosolic protein, which has a metallochaperone (or Cu shuttle) function (Fig. 1). Atox1 binds Cu released from CTR1 at the basolateral plasma membrane and transfers Cu to ATP7B and ATP7A located in the trans-Golgi network (TGN) and vesicles of the endocytic pathway [9, 10]. ATP7A and ATP7B then transfer Cu into the lumen of the secretory pathway where Cu is utilized for activation of Cu-dependent enzyme or is exported out of the cells when present in excess. The Atox1-mediated transfer of Cu to the Cu-ATPases is a subject of redox regulation by the glutathione pair (GSH-GSSG) [7]. In neuronal cells, changes in the GSH-GSSG ratio modulate the ability of Atox1 to bind Cu and thus control the amount of Cu delivered to the secretory pathway [8]. ATP7A plays a “housekeeping” role in most tissues, except the liver, where its expression is low [11]. ATP7A is especially critical for the dietary Cu uptake in the intestine and for Cu entry into the brain [12]. Mutations in ATP7A result in systemic Cu deficiency and progressive and fatal neurodegenerative disorder known as Menkes’ disease [13]. ATP7B is expressed in many tissues and is especially high in the liver, where ATP7B function is well understood. In hepatocytes, ATP7B transfers Cu to the Cu-dependent ferroxidase ceruloplasmin in the TGN and facilitates efflux of excess Cu across a canalicular membrane into the bile. In a normally functioning adult human liver, ATP7B maintains intracellular Cu levels at <50 μg Cu/g of the dry liver. Newborns have a significantly higher Cu concentration than adults [14]; in the postnatal livers, the excess Cu is sequestered within the yet-to-be-characterized vesicular compartments. Recent studies have demonstrated that ATP7B is also expressed in nonparenchymal cells of the liver, where ATP7B maintains Cu balance and may contribute to inflammatory response, when its function is lost [15]. Genetic mutations in ATP7B result in an impaired biliary efflux of Cu, an accumulation of Cu in hepatic tissues (>250–3000 μg Cu/g of the dry liver) [16], the loss of Cu incorporation into ceruloplasmin, and a spectrum of pathological changes known as Wilson disease, WD [5, 16–18]. Numerous WD-causing mutations have been identified (see the Human Gene Mutation Database (http://www.hgmd.cf.ac. uk/ac/all.php) and the Wilson Disease (WD) Mutation Database (http://www.wilsondisease.med.ualberta.ca/). The genetic studies have also uncovered higher frequency of some mutations in specific world populations and the absence of strong phenotype-genotype correlations (for recent examples, see Refs. [19–21]). Phenotypic diversity (the variable time of onset, a spectrum of presenting manifestations, and the nonuniform course of the disease) is a characteristic feature of WD. The complexity of ATP7B structure and intracellular behavior may contribute to phenotypic diversity of WD. Mutations that completely prevent protein production or cause gross structural abnormalities result in a complete loss of copper transport activity. Other mutations, while deleterious, yield protein that has residual activity and retain some aspects of its function, thus leading to a slower development of the disease. ATP7B mediates its dual role in cofactor delivery to ceruloplasmin and Cu efflux by changing its intracellular localization (for details on ATP7B function, please see Chapter 3). Under basal conditions, ATP7B is located primarily in the late Golgi/trans-Golgi Wilson Disease. https://doi.org/10.1016/B978-0-12-811077-5.00004-9 © 2019 Elsevier Inc. All rights reserved.

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FIG. 1 Copper homeostasis in hepatocyte. Copper (Cu) is transported into hepatic cells by the high-affinity copper transporter CTR1 located at the basolateral membrane. The metal then binds to cytosolic shuttles or Cu chaperones. The Cu chaperone CCS delivers Cu to cytosolic Cu- and Zn-dependent superoxide dismutase, whereas ATOX1 transfers Cu to Cu-transporting ATPase ATP7B in the secretory pathway. The glutathione pair GSH-GSSG regulates the Cu uptake by CTR1 [6] and the Cu binding by Atox1 [7, 8]. When cytosolic Cu is elevated, ATP7B leaves the TGN and traffics in vesicles toward the canalicular membrane to facilitate export of excess Cu.

network (TGN) where it transfers Cu into the TGN lumen. When Cu is elevated, ATP7B undergoes a kinase-mediated phosphorylation [22, 23] and traffics from the TGN to the apically located vesicles [24]. This process depends on myosin-V, which facilitates docking of ATP7B vesicles near the apical membrane [25]. Excess Cu is sequestered in vesicles and then exported into the bile following vesicle fusion with the plasma membrane [5, 26, 27]. ATP7B is then endocytosed and, depending on the cellular Cu levels, either returns to the pool of recycling vesicles or traffics back to the TGN. The return to the TGN is associated with ATP7B dephosphorylation by phosphatase(s), which remain to be identified. Given this complex sequence of events, it is not surprising that the disease-causing mutations often modify more than one parameter of ATP7B behavior. The involvement of other proteins (kinases, phosphatases, and trafficking machinery) adds additional level of complexity and hence potential for variability. Altogether, mutations in ATP7B can be associated with a complete loss of ATP7B synthesis, misfolding, and instability/protein degradation. The mutation may markedly diminish ATP and/or Cu binding, interfere with the protein targeting/trafficking to proper intracellular compartments, or disrupt interaction with proteins involved in ATP7B regulation/modification. In this chapter, we provide examples of these various consequences.

MOLECULAR FEATURES OF ATP7B AND CATALYTIC CYCLE ATP7B is a membrane protein, composed of multiple domains (Fig. 2A). The membrane portion of ATP7B has eight transmembrane α-helical segments. These segments form the Cu translocation pathway. The highly conserved C983PC985 motif within the sixth transmembrane segment contributes to Cu binding and translocation. Experimental mutations of these cysteines to serine residues produce the nonfunctional protein; the Cys985Tyr substitution is a WD-causing mutation. The cytosolic portion of ATP7B constitutes about 70% of protein mass and includes at least nine domains. The ATP binding and hydrolysis are mediated through the concerted action of the N (nucleotide binding) and P (phosphorylation) and A

Biochemical and Cellular Properties of ATP7B Variants Chapter

4

35

FIG. 2 Structural model of ATP7B and distribution of Wilson disease mutations in various domains. (A) ATP7B is shown as a ribbon model (generated by UCSF chimera). The cytosolic and transmembrane domains are as follows (MBD1, light gray; MBD2, light orange; MBD3, light green; MBD4, purple; MBD5, cyan; MBD6, dark gray; TM regions, yellow; A-domain, green; and ATP-binding domain, red). (B) Distribution of WD-causing mutations among the various domains of ATP7B is uneven.

(actuator) domains (Fig. 2A). ATP binds primarily within the N-domain; the conserved residues H1069, E1064, G1099, G1101, I1102, G1149, and N1150 contribute to ATP binding [40]. The substitution of invariant His1069 for glutamine (His1069Gln) is one of the most common WD mutations in Caucasian and African American populations. Other WD mutations of ATP-coordinating residues include G1099S, G1101Arg, I1102T, and G1149A. The mutations in the vicinity to the nucleotide-coordinating residues may also significantly diminish ATP binding by altering the spatial organization of the binding pocket. Following Cu binding to the transmembrane portion, the N-domain with bound ATP approaches the P-domain, and ATP phosphorylates the invariant catalytic aspartate D1027 by transferring its terminal phosphate to carboxyl side chain of the aspartate residue. The catalytic aspartate is located within the highly conserved D1027KTGT motif in the P-domain. Formation of the phosphorylated intermediate and its subsequent hydrolysis by water supplies the energy necessary for conformational transitions within ATP7B and the expulsion of Cu from the transmembrane portion into the lumen of the secretory pathway. Experimental mutation D1027 > A completely eliminates ATP7B enzymatic activity and Cu transport, highlighting the essential role of this residue. The naturally occurring substitutions of conserved neighboring residues in the immediate vicinity of the catalytic aspartate (T1029A/I and T1031S/A) are also deleterious, as evidenced by the association of these mutations with WD. The A-domain (which is also known as an “actuator” or a “transduction” domain) is thought to undergo rotation during the catalytic cycle and use its conserved T858GE860 motif to facilitate dephosphorylation of the catalytic aspartate [28]. The movements of the N-, P-, and A-domains are coupled, and although direct evidence for ATP7B is still lacking, studies from other P-type ATPases and prokaryotic Cu-ATPases indicate that these domains and the membrane part of the protein are involved in a complex network of direct and long-range interactions. Significance of the individual N-, P-, and A-domains and transmembrane domain as well as their interactions is illustrated by the fact that the vast majority of WD-causing mutations are clustered within these domains and predicted contact regions (Fig. 2B). The ATP-binding domain (N- and Pdomains) has by far the largest number of mutations followed by those in the transmembrane region and the A-domain.

PHYSICAL PROPERTIES OF ATP7B VARIANTS While a great majority of the WD-causing mutations are yet to be fully characterized, available data indicate that the amino acid substitutions within ATP7B have direct effect on protein folding, stability, and function [29]. We have used calculations of solvent-accessible surface areas (SASA) and hydrophobicity indexes (Fig. 3A and B) of individual residues

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II Molecular Mechanisms

FIG. 3 Physical properties of amino acid side chains before and after WD mutations. (A) Linear block model of ATP7B with different domains shown in ˚ 2) for residues in the wild-type ATP7B. Each vertical colors corresponding to the structural model in Fig. 2. (B) Top: solvent-accessible surface area (in A line gives a value for the amino acid residue mutated in the corresponding position in WD (the domains are identified by color according to the block model). Bottom: change in the solvent-accessible area for the residues after the mutation for each position. Negative values indicate smaller area and the decrease in volume; positive values indicate increase in the surface area taken by the mutant. The discussed SNPs are marked by an asterisk (*). (C) Top: Kyte-Doolittle hydrophobicity values for the amino acids in wild-type ATP7B and (bottom) corresponding disease mutations (color-coded according to the block model). Altogether, the data illustrate that mutations within the regulatory N-terminal domain have a general trend of decreasing the volume of side chains and thus increasing the flexibility of this region, whereas mutations in the A- and ATP-binding domains are more often associated with an increased bulk of the side chains and therefore higher probability of significant structural change. Change in hydrophobic properties occurs in both directions; mutations in the transmembrane domain show more frequent decrease of hydrophobicity, which is likely to destabilize this domain.

to predict changes caused by each of the 457 WD-causing mutations at their respective positions. To do that, we placed in silico the correct amino acid residues or the corresponding WD mutant residues in the tripeptide G-X-G [30, 31], and the surface of the tripeptide was traced by a sphere [30]. Changes in solvent accessibility compared with the wild-type ATP7B (ΔSASA) illustrate whether mutation is associated with an increase or decrease in the local protein volume (Table 1); this in turn helps to predict the effect of each mutation on protein structure and stability within the immediate vicinity of the mutation. The changes in properties of the residues (hydrophobic vs hydrophilic) caused by mutation can be determined by comparing the Kyte-Doolittle Hydropathy (KDH) indexes of amino acids before and after substitution (Fig. 3B) [32]. The KDH index scale for amino acids in their native environment ranges from 4.5 (least hydrophobic) to +4.5 (very hydrophobic) (Table 1). Like changes in the solvent accessibility, changes in hydrophobicity could disrupt existing salt bridges and hydrogen-bond networks and destabilize interactions dependent on the hydrophobic contacts. In the N-terminal metal-binding region, the mutations cause mostly decrease in protein volume in corresponding positions (Fig. 3A, bottom panel). These changes could increase protein flexibility, affect protein stability, and diminish the precision of interdomain interactions or interactions with proteins involved in ATP7B regulation [33, 34]. However, mutations of small and flexible Gly residues (such as G85 V in MBD1 and G591D in MBD6) have a marked destabilizing effect and decrease stability and folding or corresponding metal-binding domains [35, 36]. Lastly, the mutations may have only

TABLE 1 The Changes in Solvent-Accessible Surface and Hydrophobicity Index for Known WD Mutations SolventAccessible Surface Area (SASA) Mutant (ΔSASA)

SolventAccessible Surface Area (SASA)

Hydrophobicity Index

SolventAccessible Surface Area (SASA)

Hydrophobicity Index

Hydrophobicity Index

Mutant

Mutation

WT

Mutant (ΔSASA)

WT

Mutant

Mutation

WT

Mutant (ΔSASA)

WT

Mutant

0.8

0.4

Val456Leu

155

15

4.2

3.8

Cys703Tyr

135

95

2.5

1.3

45

3.5

0.8

Gln457Ter

180

0

Gln707Arg

180

45

230

70

1.3

3.5

Ala486Ser

115

Leu708Pro

170

Cys72Ter

135

135

0

Cys490Ter

135

135

2.5

Gly710Ser

75

40

0.4

0.8

Gly85Val

75

0.4

4.2

Leu492Ser

170

55

3.8

Gly710Arg

75

150

0.4

4.5

Gln95Ter

180

180

3.5

0

Gln511Ter

180

180

Asp96Gly

150

75

3.5

Gly515Val

75

Ser105Ter

115

115

0.8

Leu523Ter

170

170

Cys108Arg

135

Glu529Gly

190

115

3.5

Gln110Ter

180

180

3.5

0

Tyr532His

230

35

1.3

Gln111Ter

180

180

3.5

0

Tyr532Cys

230

95

1.3

Gln115Ter

180

180

3.5

0

Val536Ala

155

40

Ile116Thr

175

35

0.7

Pro539Leu

145

25

1.6

Arg136Trp

225

30

4.5

0.9

Glu541Lys

190

10

3.5

Arg148Trp

225

30

4.5

0.9

Gln544Ter

180

180

Gln155Ter

180

0

Leu549Pro

170

25

Cys157Phe

135

75

2.8

Ala553Glu

115

65

Gly170Val

75

80

0.4

4.2

Gly591Ser

75

40

Tyr187Ter

230

230

1.3

0

Gly591Asp

75

75

Gln188Ter

180

180

3.5

0

Val597Ile

155

20

4.2

Gln193Ter

180

180

3.5

0

Ala604Pro

115

30

1.8

Asp196Glu

150

Val606Gly

155

4.2

Leu217Ter

170

170

3.8

0

Glu611Lys

190

10

3.5

Cys271Ter

135

135

2.5

0

Gly614Cys

75

60

0.4

Mutation

WT

Ser15Gly

115

40

Asn41Ser

160

Tyr44Asn

80

30

0.4 0

2.5

4.5

4.5

3.5 2.5

3.5

3.5

0

3.5 1.8

80

80

0.8 0 0.8

25

3.5

4.5

3.8

1.6

3.5

0

Gly710Ala

75

40

0.4

1.8

0.4

4.2

Gly710Val

75

80

0.4

4.2

0

Gly711Arg

75

150

0.4

4.5

0.4

Gly711Glu

75

115

0.4

3.5

3.2

Gly711Trp

75

80

0.4

4.2

2.5

Tyr713Cys

230

95

1.3

2.5

1.8

Tyr715His

230

45

1.3

3.8

Tyr715Ter

230

Gln717Ter

180

Ala718Pro

115

30

3.8

4.2

3.5

3.9 0

– 180

3.8

3.2

3.8

1.6

4

180

2.5

180

Biochemical and Cellular Properties of ATP7B Variants Chapter

90

WT

3.2

1.3

–

3.5

0

1.8

1.6

Ser721Pro

115

30

1.8

3.5

Ala727Asp

115

35

1.8

0.4

0.8

Ala727Val

115

40

1.8

4.2

0.4

3.5

Met729Val

185

1.9

4.2

Val731Glu

155

1.6

Val731Ala

155

0.4

Leu732His

170

3.9

Leu732Pro

170

Val734Phe

155

4.5

2.5

35 40 25 25 55

4.2 4.2

4.2

1.6 3.5

3.5 1.8

2.8 Continued

37

3.8

30

0.8

1.6

38

TABLE 1 The Changes in Solvent-Accessible Surface and Hydrophobicity Index for Known WD Mutations—cont’d

WT

Gln286Ter

180

180

Gln289Ter

180

Tyr301Ter

Hydrophobicity Index

WT

Mutant (ΔSASA)

WT

Mutant

4.5

3.5

Ala736Val

115

40

1.8

4.2

30

4.5

0.9

Thr737Arg

140

85

0.7

75

40

0.4

Thr737Ile

140

35

0.7

4.5

His639Tyr

195

35

3.2

1.3

Tyr741Ter

230

1.3

0

Leu641Ser

170

55

0.8

Tyr741Cys

230

95

1.3

2.5

Asp642His

150

45

3.2

Tyr743Cys

230

95

1.3

2.5

Met645Arg

185

40

4.5

Ser744Pro

115

30

0.8

45

WT

3.5

0

Arg616Gln

225

180

3.5

0

Arg616Trp

225

230

230

1.3

0

Gly626Ala

Cys305Ter

135

135

0

Asp329His

150

Glu332Ter

190

Gly333Arg

75

45 190 150

2.5 3.5 3.5

3.2 0

0.4

4.5

Gln355Ter

180

180

3.5

0

Gln649Arg

180

Glu378Ter

190

190

3.5

0

Trp650Ter

255

Ile381Ser

175

60

Ser653Tyr

115

Ser382Cys

115

Gln388Ter

180

Glu396Gln

20

4.5

0.8

Hydrophobicity Index

Mutation

Mutation

Mutant (ΔSASA)

Hydrophobicity Index Mutant

Mutant

WT

SolventAccessible Surface Area (SASA)

45

255 115

1.8

3.8 3.5 1.9 3.5 0.9

4.5 0

0.8

Leu745Pro

170

Ile747Phe

175

35

4.5

3.8

2.8

1.6

Leu748Met

170

15

3.8

1.9

Glu754Lys

190

10

3.5

3.9

Lys755Arg

200

25

3.9

4.5

Cys656Ter

135

180

3.5

0

Ser657Arg

115

110

190

10

3.5

Met665Ile

185

10

1.9

4.5

Ala756Gly

115

Glu396ter

190

190

3.5

Leu667ter

170

170

3.8

0

Ala756Val

115

Ala399Pro

115

30

Asn676Ile

160

3.5

4.5

Arg758Met

225

Ser406Ala

115

0

0.8

1.8

Gln680ter

180

3.5

0

Pro760Leu

145

25

Pro410Leu

145

25

1.6

3.8

Pro690Leu

145

25

1.6

3.8

Phe763Tyr

210

20

Glu412Ter

190

3.5

0

Gly691Arg

75

150

0.4

4.5

Asp765Asn

150

10

3.5

3.5

Glu418Lys

190

10

3.5

3.9

Ser693Pro

115

30

0.8

1.6

Asp765His

150

45

3.5

3.2

Asp419Asn

150

10

3.5

3.5

Ser693Cys

115

20

0.8

Asp765Gly

150

3.5

0.4

Leu436Val

170

4.2

Ser693Tyr

115

115

0.8

Thr766Arg

140

85

0.7

4.5

Thr766Met

140

1.9

Ser876Phe

115

95

0.8

Thr991Met

140

45

0.7

Pro767Ser

145

Pro768His

145

Pro768Leu

145

190

15 45 30

1.8

3.8 0.7

1.6

15 180

0

25

1.6

2.5

–

2.5

1.3

230

4.5

0.8

3.5

135

WT

0.8

4.5

2.5 1.3 2.8

40 40 40

75

1.8 1.8

0.4 4.2

4.5

1.9

1.6

3.8

2.8

1.3

1.9

1.6

0.8

Asn878Lys

160

40

3.5

3.9

Pro992His

145

50

1.6

50

1.6

3.2

Thr888Pro

140

5

0.7

1.6

Pro992Leu

145

25

1.6

3.8

25

1.6

Val890Met

155

30

Thr993Met

140

45

0.7

1.9

3.8

4.2

1.9

3.2

II Molecular Mechanisms

Mutant (ΔSASA)

Mutation

SolventAccessible Surface Area (SASA)

PART

SolventAccessible Surface Area (SASA)

185

40

Met769Ile

185

10

1.9

Met769Val

185

30

1.9

Leu770Pro

170

25

3.8

Leu770Leu

170

Leu776Pro

170

25

3.8

Leu776Val

170

15

3.8

Arg778Gln

225

45

Arg778Leu

225

Arg778Gly

225

Arg778Trp

225

Trp779Gly

255

Trp779Ter

255

Glu781gly

190

Lys785Arg

200

Thr788Ile

0

1.9

3.8

55 150 30 180 –

Gly891Asp

75

75

0.4

4.5

Gly891Val

75

80

0.4

4.2

Gln898Arg

180

45

3.5

Ile899Phe

175

35

Lys910Ter

200

200

Gln914Ter

180

180

Gln915Arg

180

45

3.5

Asp918Asn

150

10

Arg919Gly

225

150 75

1.6 3.8 1.6 4.2

4.5 4.5

3.5 3.8

Val995Ala

155

40

4.2

Met996Thr

185

45

1.9

Gly998Asp

75

75

0.4

3.5

2.8

Gly1000Arg

75

150

0.4

4.5

3.9

0

Ala1003Thr

115

25

1.8

3.5

0

Ala1003Val

115

40

1.8

4.5

Gln1004Pro

180

35

3.5

3.5

Lys1010Thr

200

4.5

0.4

Lys1010Arg

200

Gly1012Arg

4.5

2.8

3.5 4.2 4.5

2.5

1.8 0.7

0.7 4.2

3.5

1.6

3.9

0.7

25

3.9

4.5

75

150

0.4

4.5

60

4.5

0.4

Phe920Cys

210

4.5

0.9

Ser921Asn

115

45

0.8

3.5

Gly1012Val

75

80

0.4

4.2

0.9

0.4

Ser921Arg

115

110

0.8

4.5

Pro1014Leu

145

25

1.6

3.8

Ile929Val

175

20

4.2

Met1017I1e

185

115

0

Ala1018Val

115

40

Lys1020Arg

200

25

1.9

Ile1021Lys

175

25

4.2

Ile1021Val

175

20

4.5

4.2

2.5

Val1024Ala

155

40

4.2

1.8

0.9 115

4.5

–

4.5

1.9

4.5

1.8

4.2

0.4

Ser932Ter

115

25

3.9

4.5

Thr933pro

140

5

0.7

140

35

0.7

Thr935Met

140

45

0.7

Leu795Arg

170

55

3.8

4.5

Leu936Val

170

15

Ala803Thr

115

25

1.8

0.7

Trp939Cys

255

120

Glu810ter

190

190

3.5

Gly943Ser

75

40

0.4

0.8

Met1025Lys

185

15

1.9

3.9

Arg816Ser

225

110

4.5

0.8

Gly943Asp

75

75

0.4

3.5

Met1025Arg

185

40

1.9

4.5

Arg827Trp

225

80

4.5

1.6

Gly943Cys

75

60

0.4

Thr1029Ile

140

35

Arg827Pro

225

80

4.5

1.6

Val949Gly

155

80

0.4

Thr1031Ala

140

Lys832Arg

200

25

3.9

4.5

Arg952Lys

225

25

4.5

3.9

Thr1031Ser

Gly836Glu

75

115

0.4

3.5

Gln963Ter

180

180

3.5

0

Pro840Leu

145

25

1.6

Ile967Phe

175

2.8

Asp842Asn

150

10

3.5

3.5

Arg969Gln

225

Gly843Arg

75

150

0.4

4.5

Arg969Trp

225

30

Thr850Ile

140

35

0.7

Ala971val

115

40

Ser855Tyr

115

115

0.8

1.3

Thr974Met

140

45

0.7

Leu856Arg

170

55

4.5

Ser975Tyr

115

115

0.8

3.8

0

3.8

4.5

35 45

3.8 0.9

1.6

2.5

4.2

4.5

3.9 4.5

4.5 3.9

0.7

4.5

25

0.7

1.8

140

25

0.7

0.8

Thr1033Ser

140

25

0.7

0.8

Thr1033Ala

140

25

0.7

50

3.2

1.8

4.5

3.5

His1034Pro

195

4.5

0.9

Gly1035Val

75

80

4.2

Val1036Ile

155

20

1.9

Arg1038Lys

225

25

4.5

3.9

Arg1041Pro

225

80

4.5

1.6

1.8

1.3

0.4 4.2

1.6 4.2 4.5

39

Continued

4

3.5

4.5

0.8

10

Biochemical and Cellular Properties of ATP7B Variants Chapter

Met769Arg

40

TABLE 1 The Changes in Solvent-Accessible Surface and Hydrophobicity Index for Known WD Mutations—cont’d

Hydrophobicity Index Mutant

Mutation

WT

Mutant (ΔSASA)

4.5

0.7

Thr977Arg

140

85

0.7

Thr977Met

140

45

0.7

0.4

Leu979Gln

170

10

3.8

1.8

0.7

Cys980Arg

135

90

4.2

0.4

Cys980Tyr

135

4.5

Ala982val Cys985Tyr

WT

Ile857Thr

175

35

Thr858ala

140

25

0.7

Glu860gly

190

115

3.5

Ala861Thr

115

Val864Gly

155

Gly869Arg

75

150

0.4

Gly869Val

75

80

0.4

25 80

Hydrophobicity Index

WT

Mutation

Ala874Pro

115

30

1.8

Ala874Val

115

40

1.8

Arg875Gly

225

Arg875Val

225

80

4.5

Serl067Asn

115

45

0.8

Glu1068Gly

190

115

His1069Gln

195

His1069Asn

195

His1069Tyr

195

Pro1070Ser

145

Ala1074Val

115

40

1.8

Cys1079Phe

135

75

2.5

Glu1082Ter

190

Leu1083Phe

170

Leu1088Ter

170

Gly1089Glu

75

115

0.4

Gly1089Val

75

80

0.4

Cys1091Tyr

135

95

1.8

4.2

WT

Mutant (ΔSASA)

Arg1041Trp

225

30

Leu1043Pro

170

3.5

Asp1047Val

150

5

3.5

4.2

2.5

4.5

Pro1052Leu

145

20

1.6

3.8

95

2.5

1.3

Leu1057Pro

170

115

40

1.8

Ala1058Val

115

40

135

95

2.5

Gly1061Glu

75

115

95

Ser986Phe

115 170

Gly988Arg

75

150

0.4

Gly988Val

75

80

0.4

3.5

Met1169Thr

185

45

1.9

3.5

0.4

Met1169Val

185

30

1.9

15

3.2

3.5

Glu1173Lys

190

35

3.2

3.5

Glu1173Gly

190

3.2

1.3

Gly1176Arg

75

1.6

0.8

Gly1176Glu

75

4.2

Thr1178Ala

2.8

35 30

190 40 170

4.5

0.4 4.2

Hydrophobicity Index

Mutation

WT

Leu987Pro

150

1.6 4.2

SolventAccessible Surface Area (SASA)

25

4.5 1.9

4.2 1.3 2.8

25

25

WT 4.5 3.8

3.8 1.8 0.4

0.9 1.6

1.6 4.2 3.5

Ala1063Val

115

40

1.6

Glu1064Lys

190

10

4.5

Glu1064Ala

190

Ala1065Pro

115

30

Gly1266Glu

75

115

0.4

3.5

Gly1266Val

75

150

0.4

4.5

4.2 0.7 4.2

75

1.8

Mutant

3.5 3.5 1.8

4.2 3.9 1.8 1.6

3.5

3.9

Gly1266Trp

75

150

0.4

4.5

3.5

0.4

Asp1267Asn

150

10

3.5

3.5

150

0.4

4.5

Asp1267Ala

150

115

0.4

3.5

Asp1267Val

150

140

25

0.7

Gly1268Arg

75

Leu1181Pro

170

25

0

Ala1183Thr

115

3.8

2.8

Ala1183Gly

115

3.8

0

Ile1184Thr

175

Gly1186Ser

75

40

0.4

Gly1186Cys

75

60

0.4

Ala1193Pro

115

30

3.5

2.5

3.5 4.2 1.3

10

0.8 3.8

Mutant

115

1.8

35

3.5

1.8

5

3.5

4.2

150

0.4

4.5

20

3.5

0.7

3.8

1.6

Asn1270Thr

160

1.8

0.7

Asp1271Asn

150

10

3.5

3.5

40

1.8

0.4

Pro1273Gln

145

35

1.6

3.5

35

4.5

0.7

Pro1273Leu

145

25

1.6

0.8

Pro1273Ser

145

Ala1274Thr

115

25

1.8

Ala1274Val

115

40

1.8

25

1.8

2.5 1.6

30

1.6

3.8 0.8 0.7 4.2

II Molecular Mechanisms

Mutant (ΔSASA)

SolventAccessible Surface Area (SASA)

PART

SolventAccessible Surface Area (SASA)

Phe1094Leu

210

40

Ala1197Thr

115

25

Gln1095Pro

180

35

3.5

1.6

Gln1200Pro

180

35

Pro1098Arg

145

90

1.6

4.5

Gln1200Ter

180

180

Gly1099Ser

75

40

0.4

0.8

Ala1202Gly

115

40

Glyl10lArg

75

150

0.4

4.5

His1207Arg

195

35

2.8

3.8

30

1.8 3.5 3.5

3.2

175

4.5

0.7

Gly1213Val

75

80

0.4

135

90

2.5

4.5

Asp1215Tyr

150

80

3.5

Cys1104Phe

135

75

2.5

2.8

Val1216Met

155

30

Val110611e

155

20

4.2

4.5

Thr1220Met

140

45

0.7

Val1106Leu

155

15

4.2

3.8

Gly1221Glu

75

115

0.4

Val1106Asp

155

5

4.2

3.5

Asp1222Asn

150

10

3.5

Gly1111Asp

75

75

0.4

3.5

Asp1222Val

150

5

3.5

Gly1111Ala

75

40

0.4

1.8

Asp1222Tyr

150

80

3.5

Leu1120Ter

170

170

3.8

0

Arg1228Thr

225

85

4.5

Val1140 Ala

155

40

4.2

1.8

Arg1228Ter

225

225

Gln1142His

180

Ile1230Val

175

20

Gln1142Ter

180

0

Thrl232Pro

140

5

0.7

Val1146Met

155

1.9

Gln1233Pro

180

35

3.5

Ile1148Thr

175

0.7

Val1234Phe

155

55

Gly1149Glu

75

115

0.4

3.5

Ile1236Thr

175

35

4.5

Gly1149Ala

75

40

0.4

Val1239Gly

155

80

4.2

Arg1151His

225

30

4.5

Ala1241Val

115

40

Arg1151Cys

225

90

4.5

Pro1245Thr

145

5

1.6

Trp1153Arg

255

30

0.9

Lys1248Asn

200

40

3.9

Trp1153Cys

255

120

0.9

Ala1250Gly

115

40

Leu1154Pro

170

25

1.6

Val1252Ile

155

20

4.2

Arg1156His

225

30

3.2

Leu1255Ile

170

5

3.8

Gly1158Val

75

80

0.4

Gln1256Arg

180

45

Asp1164Asn

150

10

3.5

3.5

Lys1258Ter

200

Ala1168Pro

115

30

1.8

1.6

Val1262Phe

155

55

Ala1168Ser

115

0

1.8

0.8

Gly1266Arg

75

150

15 180 30 35

3.5 3.5 4.2 4.5

3.8 4.5

3.2

1.8 3.2 2.5 4.5 2.5

4.2

200

4.2

4.5 4.5

4.2

1.8

180

1.6

Ala1278Gly

115

40

Ala1278Val

115

0.4

Asp1279Gly

150

4.5

Asp1279Tyr

150

4.2

40 75 80

3.5

0

1.8 1.8

0.4 4.2

3.5

0.4

3.5

1.3

Gly1281Asp

75

75

0.4

Gly1281Cys

75

60

0.4

1.9

Gly1287Ser

75

40

0.4

0.8

1.9

Gly1287Arg

75

150

0.4

4.5

3.5

Thr1288Arg

140

85

0.7

4.5

3.5

Thr1288Met

140

45

0.7

Glu1293Lys

190

10

3.5

1.3

Ala1295Asp

115

35

0.7

Asp1296Asn

150

10

0

Val1297Ile

155

20

4.2

4.2

Val1297Asp

155

5

4.2

1.6

Val1298Ile

155

20

4.2

4.5

1.6

Val1298Leu

155

15

4.2

3.8

Leu1299Phe

170

40

3.8

2.8

0.7

Leu1304Phe

170

40

3.8

2.8

0.4

Leu1305Pro

170

Ala1309Val

115

40

0.7

Ser1310Arg

115

110

0.8

3.5

Ser1314Cys

115

20

0.8

2.5

0.4

Arg1319Ter

225

225

4.5

0

4.5

Arg1320Ser

225

110

4.5

0.8

4.5

Arg1322Pro

225

80

4.5

1.6

Asn1324Ser

160

45

3.5

0.8

0

Leu1327Val

170

15

2.8

Ala1328Thr

115

Leu1329Pro

170

1.3

4.2

2.8

4.2

1.8

3.5 3.9

180

4.5

25

3.5 2.5

1.9 3.9

1.8

3.5

3.5

3.5 4.5 3.5

3.8 1.8

3.8

1.6 4.2 4.5

4.2

Biochemical and Cellular Properties of ATP7B Variants Chapter

Ile1102Thr

Gln1277Ter

0

1.8

Cys1104Arg

0.7

4

4.2

4.5

25

1.8

0.7

3.8

1.6 Continued

41

0.4

25

42

TABLE 1 The Changes in Solvent-Accessible Surface and Hydrophobicity Index for Known WD Mutations—cont’d Solvent Accessible Surface Area (SASA) Mutant (ΔSASA)

WT

Mutant

Tyr1331Ser

230

115

1.3

Tyr1331Cys

230

95

1.3

Asn1332Lys

160

Asn1332Asp

160

10

Val1334Asp

155

5

Gly1335Arg

75

150

Ile1336Thr

175

Gly1341Ser

75

40

0.4

0.8

Gly1341Arg

75

150

0.4

4.5

Gly1l341Asp

75

75

0.4

Gly1341Val

75

80

0.4

Ile1348Asn

175

15

Gln1351Ter

180

180

Pro1352Arg

145

90

1.6

Pro1352Leu

145

25

1.6

Pro1352Ser

145

30

1.6

0.8

Trp1353Arg

255

30

0.9

4.5

Trp1353Ter

255

255

0.9

Gly1355Ser

75

40

0.4

0.8

Gly1355Asp

75

75

0.4

3.5

Gly1355Cys

75

60

0.4

Ala1358Ser

115

0

Met1359Ile

185

10

1.9

4.5

Met1359Val

185

30

1.9

4.2

Ser1363Phe

115

Leu1368Pro

170

40

35

25

2.5

Hydrophobicity Index

WT

Mutant (ΔSASA)

WT

Mutant

Ser1431Tyr

115

115

0.8

Ser1432Phe

115

95

0.8

2.8

0.7

1.9

1.3

3.5

3.9

Thr1434Met

140

45

3.5

3.5

Ala1445Pro

115

30

1.8

1.6

3.5

Ter1466Arg

–

225

–

4.5

4.2 0.4

4.5

4.5

0.7

3.5 4.2

4.5 3.5

1.8

95

0.8

Solvent Accessible Surface Area (SASA)

Mutation

0.8 3.8

3.5 0 4.5 3.8

0

2.5 0.8

2.8 1.6

II Molecular Mechanisms

WT

Hydrophobicity Index

PART

Mutation

Ser1369Leu

115

55

Leu1373Pro

170

Leu1373Arg

170

Gln1372Ter

180

180

Leu1373Pro

170

25

3.8

1.6

Cys1375Ser

135

20

2.5

0.8

Pro1379Ser

145

30

Met1392Lys

185

Trp1410Ter

255

25 55

15 255

0.8

3.8

3.8

1.6

3.8

4.5

3.5

0

1.6

0.8

1.9 0.9

3.9 0

Amino acid properties of 450 Wilson disease mutations are listed. The solvent-accessible surface area measurements were calculated for the residue X in the tripeptide G-X-G (as described in Refs. [30, 31]). The hydrophobicity index values for the wild-type and mutant residues are values calculated according to the hydrophobicity scale of Kyte and Doolittle [32].

Biochemical and Cellular Properties of ATP7B Variants Chapter 4 43

44

PART

II Molecular Mechanisms

minor, if any, effect on protein volume or hydrophobicity but alter the charge of the amino acid residue. Such mutations are likely to be less disruptive of protein function and may be associated with a milder disease phenotype. For example, N41S mutation, which does not significantly affect the volume occupied by this residue nor changes the hydrophilic nature of the residue in this position (Table 1), results in ATP7B variant that retains the Cu transport activity. The association of this mutation with Wilson disease could be due to the loss in the ability of ATP7B-N41S to faithfully traffic to the canalicular membrane and respond to changes in copper concentration (ATP7B-N41S traffics to basolaterally located vesicles [37]). The initial report on identification of this mutant does not describe whether the mutation was homozygous; therefore, it is also possible that the negative effect of ATP7B-N41S substitution is apparent only if another deleterious mutation is present on a second allele of ATP7B gene. The transmembrane helical regions are largely hydrophobic owning to their embedding in the lipid bilayer. Wilson disease mutations in the TM region(s) cause reduction in solvent accessibility in a large number of codon positions (Fig. 3B, bottom). The mutants are also more hydrophilic in nature when compared with the wild type (Fig. 3C (bottom), which has a destabilizing effect on the hydrophobic helical segments in a lipid bilayer and in turn affects normal function of the pump or its intracellular sorting. The Cys985Y (C983PC985 motif in TM 6) substitution not only would prevent Cu(I) coordination but also could destabilize the helical bundle packing with its increased volume mutation. Mutations in the Adomain and the ATP-binding domains show visibly large-scale shifts in surface area but modest changes in the hydrophobicity scale (Fig. 3B and C). Compared with the wild type, the SASA values for the mutants indicate that the residues are more buried and less accessible to salt bridges and or other interactions. Since both A-domain and the ATP-binding domains undergo significant motions and changes in the interdomain contacts during ATP binding and hydrolysis, such mutations may have an adverse effect on catalytic phosphorylation.

WILSON DISEASE MUTATION IN VARIOUS DOMAINS Yeast complementation system relies on the ability to restore the growth of Cu transport-deficient yeast strain by the expression of ATP7B or variants. This system has been used successfully to classify loss-of-function mutation from less severe mutations [38–41]. In combination with the studies of ATP7B variants in mammalian cells [41], this approach allows a fairly rapid initial characterization of a large number of mutants. A more laborious study directly measuring copper transport activity of 28 Wilson disease mutations along with the analysis of their enzymatic and cellular properties has also been published [29]. This study revealed that a significant fraction of ATP7B variants associated with Wilson disease has small but measurable transport activity (which also explains why some of the mutants may sustain cell growth in a yeast complementation assay). This finding is significant. Wilson disease is an autosomal recessive disorder (i.e., disorder, in which both copies of the ATP7B gene must be mutated for pathology to develop). Thus ATP7B proteins with various combinations of mutations will have various degrees of residual transport activity, which may in turn affect disease onset and progression.

Mutations in the N-Terminal Domain Are Rare But Have Significant Consequences The N-terminal domain of human ATP7B is the most structurally diverse region of the protein, when ATP7B is compared with orthologues from other species. The N-terminal domain contains six metal-binding domains (MBDs), each with a conserved CxxC site for binding Cu(I) [28, 29, 42–47] (Fig. 2A). Each MBD has a ferredoxin fold and connected to other MBDs by loops of variable lengths. The loops allow the N-terminal domain flexibility necessary to rearrange upon copper transfer from the copper chaperone Atox1 [48]. The N-terminal domain also interacts with the neighboring cytosolic ATPbinding domain (and regulating the affinity for ATP) and A-domain, by perhaps forming a scaffold. Studies of the isolated domains have shown that interactions between MBDs and the ATP-binding domain are inhibitory [42, 49, 50]. While the atomic model of full length ATP7B remains to be unraveled, the solution structures of MBD1, MBD2, MBD3-MBD4, and MBD5-MBD6; the A-domain; and the nucleotide-binding domain of ATP7B have been determined [28, 50–53] contributing valuable insight. Indeed, structures of isolated domains from ATP7B and prokaryotic homologues have already been used as a model system to study the impact of Wilson disease mutations [28, 53–56]. The first 63 amino acids in the N-terminus of the ATP7B contain a short segment required for Cu-dependent trafficking of ATP7B from the TGN to the apical membrane [23, 45]. Mutations in this region lessen retention of ATP7B to the TGN under basal conditions and cause accumulation in vesicles in the vicinity of the basolateral membrane, instead of trafficking to the apical membrane [23, 45]. This abnormal ATP7B trafficking in the absence of Cu is likely to diminish incorporation of Cu into ceruloplasmin and prevent export of Cu into the bile. Three WD-causing mutations have been identified in this region—S15G, N41S, and Y44N. Biochemically, the mutations decrease the volume of the side chain and increase the

Biochemical and Cellular Properties of ATP7B Variants Chapter

4

45

hydrophilicity of the region (Fig. 3A and B). Since the region including these mutations is predicted to be unstructured, the likely explanation for the disruptive effect of mutations is the loss of interactions between this segment and other domains of ATP7B or regulatory proteins. Indeed, recent NMR studies have demonstrated that the peptide corresponding to Nterminal region interacts with the nucleotide-binding domain of ATP7B and remains associated with ATP7B even after the proteolytic cleavage within the N-terminal region [57]. The entire N-terminus, which encompasses all six MBDs, has 64 mutations, out of which 25 are codon termination mutants (not discussed) (Fig. 3A and B). Mutations of cysteine residues within the CxxC copper-binding sites would abolish copper binding and may negatively impact copper transfer to the TM regions. The C157F substitution in MBD2 is an example of such WD-causing mutation. The loss of copper binding by MBD2 was previously shown to prevent copper transfer from the cytosolic copper chaperone Atox1 to ATP7B and inhibit ATP7B activity [58]. Other disease mutations in MBDs are mostly located outside the CxxC metal-binding motifs and may alter folding of MBDs and destabilize the entire ATP7B. This idea is supported by the fact that the experimental deletion of the N-terminal segment, which includes up to five MBDs, does not inhibit ATP7B. Therefore, the negative effect of mutations within the N-terminal region is likely due to abnormal folding or disrupted regulation. Characterization of mutations G85 V, L492S, R616W, G626A, and M645R revealed disruptions in normal ATP7B function [29]. Mutations G85 V in MBD1 and L492S in MBD5 show neither catalytic nor copper transport activity [42]. The effect of G85 V substitution can be easily explained. Gly85 is a conserved residue, and its location ensures flexibility of protein in this position (Fig. 3). Substitution of a small flexible glycine with a large bulky valine affects protein stability of MBD1 and the entire ATP7B [34, 35]; the unfolding/thermal instability of MBD1 would also alter interactions between MBD1, MBD2, and MBD3, which are important for Atox1-mediated copper transfer [36, 48, 57, 59]. The strong negative effect of L492S on ATP7B function is harder to understand. L492 is located seven residues away from the CxxC site of MBD5 and is unlikely to affect copper binding. The side chain of Leu492 is oriented inwardly, and the mutation to a smaller and more hydrophilic Ser may have some effect on protein structure/MBD folding. However, the ATP7B variant with this mutation shows high level of expression, arguing against significant protein unfolding/instability [29]. Therefore, why the marked negative effect on ATP7B activity is so dramatic is unclear. These uncertainties in predicting effect of mutations (even when structures of individual domains are available) highlight the need for the high-resolution structure of the entire ATP7B, which would reveal details of protein environment and more detailed functional analysis of the mutants. Mutation R616W (in MBD6) causes hyperphosphorylation, that is, the decreased ability to cleave phosphor-aspartate intermediate during ATP hydrolysis. The low transport activity of R616W variant is consistent with the idea that mutant ATP7B is trapped in one conformation and cannot proceed normally through the catalytic cycle. Similarly, the mutation G626A did not have any loss in catalytic phosphorylation, but had partial transport activity. The M645R (in the segment connecting MBD6 and TM1) has been identified as a WD-causing mutant in several studies and is particularly common in Spanish population [60–62]. Yet, the in vitro analysis of this variant suggests that the copper transport activity of this variant is only slightly decreased. Lower expression of this variant in studies in mammalian cells suggests that the negative consequences of this mutation could be due to decreased protein abundance [29, 34]. As we discussed previously [63], it is also possible that M645 substitution has to be accompanied by a highly deleterious mutation on the second allele of ATP7B (such as deletions or stop codons) for disease phenotype to develop.

Actuator (A-Domain) and ATP Binding Domains (ATPBD) Are Major Targets of WD Mutations ATP7B belongs to a large family of ATP-driven ion and lipid transporters called P-type ATPases. The calcium-transporting ATPase sarcoplasmic-endoplasmic reticulum calcium (SERCA) is the well-characterized member of this family; SERCA and ATP7B both hydrolyze ATP to transport their respective metals and show significant structural similarity for their A-, N-, and P-domains. In the SERCA, the actuator domain (A-domain) and ATP-binding domain (N- and P-domains together) interact with each other [64]. This interaction is necessary to facilitate conformational transitions of the protein during transport cycle. In ATP7B, A-domain and ATPBD are mutated in 34 and 165 positions, respectively. The P840L, I857T, and A874V substitutions in the A-domain have been characterized and found to inhibit transport activity and show high levels of phosphorylation of catalytic aspartate. These results are consistent with ATP7B being trapped in phosphorylated state and unable to hydrolyze the phosphate to yield energy for copper translocation across membrane. Changes in the interactions between the A-domain with the ATP-binding domain would explain the phenotype [29]. Analysis of the solvent-accessible surface area for two of these mutants and for several other mutations in the A-domain shows an increase in the surface area (a potentially destabilizing prospect, Table 1). Overall, the hydrophobicity of the 34 mutations is lower (Fig. 3A and B). High abundance of the disease-causing mutants in the ATPBD highlights functional importance of this region (Fig. 2B). Several ATP7B mutants have been extensively characterized for structural defects, changes in transport activity,

46

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localization, and trafficking revealing broad spectrum of abnormalities [28, 29, 40, 65]. The P-domain mutants P992L, T1031S, and P1052L caused low transport activity and Cu uptake but did not fully eradicate the enzyme function [29]. The G1213 V mutation is located in the “hinge” region, which connects the N- and P-domains, and inhibits copper transport activity. This effect is most likely caused by the disruption of a coordinated movement of the P- and N-domains, which is necessary for phosphorylation of the catalytic aspartate in the DKTGT motif [29]. In support of this hypothesis, molecular dynamics simulation on the G1213 V mutant revealed marked changes of the normal mode motions around the hinge region [55]. Mutants D1222V and G1266R have low transport activity and render the enzyme completely inactive due to the inability of the enzyme to form a phosphorylated intermediate. These mutants are located close to the conserved D1027KTGT site and could obstruct the phosphorylation site due to the presence of a large hydrophobic group (D1222 > V) or an increase in volume and addition of a positively charged guanidine group (Fig. 3A and B). Mutations in the N-domain affect protein folding and stability, ATP binding, and protein localization. The mutants H1069Q (discussed further below) and E1064K directly affect ATP binding. The negatively charged oxygen atoms in the glutamate E1064 coordinate the positive nitrogens in the adenosine moiety, whereas the histidine residue in position 1069 is involved in π-π stacking interactions with the adenosine ring stabilizing the ATP molecule [54]. NMR studies of the isolated N-domain with the E1064A mutation showed that the mutated protein is stable and retains the overall fold of the domain, but the positions of the α-helical segments were altered, creating a more open structure, misaligning the ATPcoordinating residues, and a complete loss of ATP binding [28]. Two other mutations R1151H that are located proximally to the H1069 site and C1104F that is located further away from the ATP-binding pocket were characterized using isothermal titration calorimetry studies. These studies showed that R1151H affected ATP-binding affinity and C1104F significantly affected protein folding [66]. The mutant L1083F is facing away from the ATP-binding pocket at the surface of the N-domain. In vitro, the mutant has only partial disruption to the transport activity and does not affect catalytic phosphorylation [29]. Yet, in cells, this mutant is trapped in the ER, and inability to reach the trans-Golgi network and vesicles would account for the WD phenotype associated with this mutation. These properties suggest that the residue L1083 may play an important role in the interdomain interactions necessary for structural integrity of ATP7B associated with its exit from the ER. Given recent finding that ATP7B forms a dimer, which persist when ATP7B traffics through the secretory pathway [67], it would be interesting to test whether the L1083F substitution may disrupt dimer formation.

The H1069Q Mutant The H1069Q substitution is by far the best characterized WD mutation. This substitution causes decrease in ATP7B stability and retention in the ER [65, 68]. The mutation is most commonly found in Caucasian and African American patients [69–71]. Studies using yeast complementation showed that mutations to H1069 impaired the ATP7B function [65, 72, 73] and a significant inhibition of transport was confirmed by direct measurements of ATP7B copper transport activity [29]. The loss of this activity is likely due to the inability of the mutant to form a phosphorylated intermediate in the presence of ATP [74], which in turn could be a result of diminished affinity for ATP [66, 74]. Structural studies of the N-domain confirmed the role of H1069 in ATP binding [49, 50] but did not provide a clear answer why this mutation markedly decreases ATP7B stability. Molecular dynamics simulation studies using the NMR ensemble of the wild type and the mutant Ndomain revealed differences in ATP orientation and coordination environment that may explain diminished binding [53]. These studies also showed that the histidine residue at position 1069 was vital for the proper orientation of ATP in the binding pocket. Further structural characterization of H1069Q showed large-scale destabilization of the mutant in vitro confirming that the structural instability of the N-domain is the primary reason for instability of entire ATP7B [28].

The Mutations Within the TM Domain Revealed Long-Range Interactions Between Different Parts of ATP7B The transmembrane region of ATP7B contains eight transmembrane (TN) helical segments; they contain highly conserved residues that could coordinate Cu ions, especially TM4 and TM8; they also act as conduits for converting the 32 kJ/mol of energy acquired from ATP hydrolysis into movements associated with copper transport. Over 170 mutations have been identified within the TM domain, and they were found in all eight segments (Figs. 2B and 3). Only a handful has been well characterized. The mutation within predicted Cu-binding site cys-pro-cys (CPC) motif (C985Y) removes the side chain essential for copper binding replacing it with the bulky and hydrophobic residue further disrupting the copper translocation pathway; these changes account for the loss of ATP7B function. Mutations P760L, D765N, and M769 V in TM4

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decrease Cu transport activity but allow the formation of phosphorylated intermediate [29]. The hydrophobic nature of the replaced residues in TM domain is mostly preserved by mutations (Fig. 3A and B), but variation in the volumes of side chains can destabilize TM domain or preclude conformational transitions necessary for transport. No information is currently available of how the TM domain of ATP7B interacts with lipids and which mechanisms enable sorting of ATP7B within the TGN. Further studies are needed to examine these properties of ATP7B and the effect of mutations. The S653Y mutant is an interesting example of a TM region mutation, which retains some Cu transport activity (and hence the delivery of Cu to ceruloplasmin) but lacks the ability to traffic from the TGN under elevated Cu conditions. The ATP7B-S653Y mutant is stable and is targeted normally to the TGN [37]. Experimental mutations in this region and molecular dynamics simulations revealed that replacing Ser653 with the bulky or charged residues modifies the local electrostatic environment and induces distortions within the TM1 and neighboring TM2 [37]. Although the distortion was local and did not significantly affect the TM segments directly involved in copper binding and transfer (TM4, TM7, and TM8), the structural change in TM1 altered the properties of the N-terminal domain, which is directly connected to TM1. Specifically, the mutation of N41, which in earlier studies was shown to cause constitutive trafficking (see above), in combination with the S653Y mutation did not have an effect. This is a very intriguing example of “canceling” effect of two WD-causing mutations and yet another demonstration of complexity and variety of effects. Although the presence of two or three mutations in the same allele is rear, such multiple mutations occur, and their effect may not necessarily be additive, as the above example demonstrates.

SINGLE NUCLEOTIDE POLYMORPHISMS MAY PLAY A LARGER ROLE IN DISEASE THAN PREVIOUSLY THOUGHT Single nucleotide polymorphisms (SNPs) are the largest source of sequence variation in humans. However, contribution of SNPs to disease progression and manifestations is not well understood. SNPs are defined as genetic changes that are present in >1% of the general population [75]. Perhaps, due to this fact, SNPs have long been considered benign, and their contribution to disease phenotype has been understudied. Recently, SNPs have become a growing topic of interest. Dozens of SNPs have been identified in the ATP7B gene, and several of these are considered common, such as G2495A (Lys832Arg), C1366G (Val456Leu), and G1216 T (Ala406Ser) (highlighted as (*) in Fig. 3B) [76, 77]. Interestingly, some of these SNPs frequently show up in WD patients. For example, the Lys832Arg SNP has been reported in WD patients in over 20 studies archived in the Wilson Disease Mutation Database. The first study addressing the biochemical and cellular properties of ATP7B SNPs was published in 2011. The studies illustrated a fine line between some polymorphisms and a disease mutation. The ATP7B Gly875Arg variant was considered an SNP but was also known as a WD-causing mutation in Indian population [78]. The protein folding of ATP7B875Arg (a less common variant) was very sensitive to cellular copper levels. In low copper, ATP7B875Arg was trapped in endoplasmic reticulum and unable to reach its normal Golgi localization and activate copper-dependent enzymes. By contrast, a more common ATP7B875Gly was less sensitive to copper depletion and targeted normally. Upon copper supplementation and excess, both ATP7B875Arg and ATP7B875Gly behave very similarly [78]. These results suggest that SNPs can have different “background” effects and exacerbate effects of WD mutation under certain conditions. Direct functional studies of two other variants found that Val456Leu and Lys832Arg SNPs produce ATP7B with lower Cu transport activity [29]. More recently, Lys832Arg was studied in Drosophila melanogaster and was shown to be identified as a loss-of-function SNP. However, flies have only one copper transporter, ATP7, that shares homology with both ATP7B and ATP7A [79]. Expression of a Lys832Arg SNP construct in knockout ATP7 flies did not rescue larval death. Although these data are intriguing, the relevance of findings to human cells is uncertain. Four ATP7B SNPs were identified in the Indian population as useful predictive diagnosis markers for WD [80]. Additionally, a link has been suggested between two ATP7B SNPs (Lys832Arg and Arg952Lys) and increased the amount of bioavailable copper in Alzheimer’s disease (AD) patients [81]. Interestingly, these SNPs are found at high frequencies in the normal population, but AD patients are more likely to be homozygous for these SNPs compared with healthy controls [82]. These studies have raised important questions about the contribution of SNPs in disease risk and progression. The effects of SNPs on the protein could be most significant when the SNP is located in a functionally significant domain, such as the ATP-binding domain in ATP7B (Fig. 2B, ATPBD shown in red). It is also possible that SNPs become significant under certain metabolic conditions or in response to aging when a decreasing protein quality control may exacerbate SNPdependent changes of ATP7B properties. There is much to be learned about the impact of SNPs on ATP7B structure or function.

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CONCLUSIONS Wilson disease mutations affect all functional domains of ATP7B and have a broad spectrum of consequences. The mutational “landscape” highlights functional significance of different domains and identifies the ATP-binding domain as being most commonly targeted by substitutions. Specific location of WD mutations in ATP7B domains and changes in the volume, surface area, and hydrophobicity index of the side chains allow predictions of the potential impact of mutations on protein structure and activity. Nevertheless, direct and detailed characterization of mutations is needed, because the available data for currently characterized mutants show a broad spectrum of changes in stability, ligand-binding enzymatic and transport activity, and cellular behavior, all of which cannot be predicted by in silico analysis. Finally, emerging data on SNPs suggest that normal genetic variability could further modify properties of ATP7B and modulate effects of the diseasecausing mutations.

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