Protein structures

APPENDIX

PROTEIN STRUCTURES Understanding of the molecular mechanisms that underpin bioenergetics continues to advance as more 3-D structures of proteins are determined. Some of these structures are illustrated in this book (especially in Plates A to K) but many more are now available. These can be accessed on the Protein Data Bank (PDB) http://www.rcsb.org. Each structure is given a code. A selection of such codes, together with the proteins they refer to, are given below for proteins that are relevant to the subject matter of this book. Where the protein is not described in the text, brief details of interesting features are noted. A very valuable compilation of protein structure/function information for many of the metalloproteins discussed in this book can be found in Handbook of Metalloproteins, Volumes 1 and 2, edited by A. Messerschmidt, R. Huber, T. Poulos and K. Wieghardt and published by J. Wiley in 2001. *Indicates periplasmic location in bacteria Protein

Code

Comments

A. Respiratory electron transfer proteins." (Chapter 5) Amine dehydrogenase

1JMX

Azurin

4AZU

*A quinohemoprotein with a novel cross-linked active site cysteine tryptophylquinone and three novel thioether cross links. From Pseudomonas putida; passes electrons to c-type cytochromes or cupredoxins -

Carbon monoxide dehydrogenase (aerobic)

1QJ2

*Type 1 copper protein mainly/3 sheet structure Has active site Mo co-ordinated by 1MCD (molybdopterincytosine dinucleotide) and an S-selenylcysteine. Associated with proteins carrying Fe/S centres and FAD. Feeds electrons into a CO-insensitive respiratory chain

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3

Protein

Code

Comments

Cytochrome aa3 oxidase

1AR1

Two subunits of Paracoccus denitrificans enzyme

Cytochrome aa3 oxidase

1OCC

Bovine heart enzyme oxidized

Cytochrome ba3 oxidase

1EHK

A distinctive oxidase from the thermophile Thermus thermophilus

Cyt0chrome bcl complex

1BCC

Chicken heart

Cytochrome bcl complex

1BE3

Bovine heart

Cytochrome bcl complex

1BGY

Bovine heart

Cytochrome bcl complex

1E2V

Yeast

Cytochrome c

1HRC

Mitochondrial from horse heart

Cytochrome c2

2CXB

*Rhodobacter sphaeroides

Cytochrome c3

2CYR

*A tetra heme c-type cytochrome found in sulfate reducing bacteria

Cytochrome c peroxidase

1EB7

*From Pseudomonas aeruginosa; is a diheme c-type cytochrome A b-type cytochrome from the inter-membrane space of yeast mitochondria

2CYP

Cytochrome c550

1COT

*Paracoccus denitrificans

D. lactate dehydrogenase

1FOX

Peripheral membrane protein from E. coli

DMSO (dimethylsulphoxide) reductase

1CXS 1DMR 4DMR 1DMS 1EU1

*Has active site Mo co-ordinated by two MGD (molybdopteringuanosine dinucleotide) molecules, each of which provides two sulfur ligands; other ligands to Mo vary

Formate dehydrogenase

1KQF

See Plate E

Fumarate reductase

1FUM 1QLA 1D4E

See Plate E *A flavo c-type cytochrome enzyme from Shewanella putrefaciens

Hydrogenase

2FRV

*From Desulfovibrio gigas has a Ni-Fe active site. Donates electrons to cytochrome c3

Hydroxylamine oxidoreductase

1FGJ

*Trimeric enzyme that catalyses oxidation of hydroxylamine to nitrite. Has eight c-type hemes per polypeptide one of which, with a cross-link to a tyrosine, forms the active site. Found in Nitrosomonas bacteria

APPENDIX

28,5

Protein

Code

Comments

Methanol dehydrogenase

1H4I

*Active site PQQ within an eight bladed/3 propeller

Methylamine dehydrogenase

2BBK

*Contains two cross-linked and modified tryptophans at active site within a seven bladed /3 propeller

Methyl-coenzyme M reductase

1MRO

Contains Ni at active site as part of F430

Nitrate reductase (periplasmic-Nap)

2NAP

*Contains active site Mo bound by two MGD molecules

Nitrite reductase with five c-type hemes

1QDB

*Ammonia is reaction product. Unusual CXXCK heme binding motif at active site

Nitrite reductase cytochrome cdl

1AOF 1QKS 1NIR

*Nitric oxide is reaction product; c-type cytochrome domain accepts electrons from c-type cytochrome or cupredoxins and is o~helical; the specialized active site d I heme is located within an eight bladed/3 propeller structure. Differences in structure between the enzymes from Pseudomonas aeruginosa and Paracoccus pantotrophus; the latter undergoes a remarkable conformational change upon reduction From P. pantotrophus reduced From P. pantotrophus oxidized From P. aeruginosa oxidized

Nitrite-reductase Cu-type

1AFN

*Nitric oxide is reaction product. A trimer. Three type 1 Cu ions act as the electron acceptors from other proteins; three type 2 Cu ions are at the active sites

Nitrous oxide reductase

1QNI 1FWX

*Contains both CUA site seen in cytochrome aa 3 oxidase plus a novel active site Cuz with 4 Cu bridged by an S atom. The active site is enclosed in a seven-bladed/3-propeller structure. From Pseudomonas nautica and P. denitrificans

Pseudoazurin

3PAZ 8PAZ

*Type 1 copper protein- mainly ]3 sheet structure. Oxidized and reduced forms from Alcaligenes

faecalis

286

BIOENERGETICS3

Protein

Code

Comments

Rusticyanin

1A8Z

*Type 1 Cu protein from

Sulfite oxidase

1SOX

Chicken liver from intermitochondrial space. Active site Mo co-ordinated by a pterin

TMAO (Trimethylamine-N-oxide) reductase

1TMO

*From Shewanella massilia; has active site Mo co-ordinated by two MGD groups

T. ferrooxidans

B. Photosynthetic proteins: (Chapter 6) Bacteriorhodopsin

1C3W

Bacteria photosynthetic reaction centre

1PCR 2PRC

From R. sphaeroides From R. viridis

Cytochrome-f

1HCZ

Unusual c-type cytochrome with /3-sheet structure

Halorhodopsin LHCII LH2

1El2 Not deposited 1K2U

Photosystem 1

1JBO

Photosystem 2

1FE1

Plastocyanin

lAG6 7PCY

From spinach

Bovine heart F1

1BMF

The original 2.8 A structure of the F l part

Bovine heart F I

1E79

Contains the central stalk region originally not seen (2.4 A)

Bovine heart F l

1H8E

A form with all catalytic sites occupied

Spinach Circular O~9/~9 structure

R. acidophilia From S. elongatus From S. elongatus

C. ATP synthase: (Chapter 7)

Bovine heart F1 inhibitor

1GMU

Coiled coil

E. coli: F1 ~ subunit

1ABV

N-terminal domain

Thylakoid F1

1KMH

Has inhibitor tentoxin bound

Yeast F a + c ring

1QO1

3.9 A resolution but shows ring of 10 c subunits

D. Transport proteins." (Chapter 8) E. coli glycerol facilitator

1FX8

A passive facilitation of the cytoplasmic membrane

E. coli Msb protein

1JSQ

First structural information at 4.5 A resolution for an ABC-type ATPase. A homodimer with each subunit providing six trans-membrane ce helices and a nucleotide-binding domain. The helices pack so as to provide a chamber that is exposed to the cytoplasmic half of the bilayer