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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 struc-
ture 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 pro-
tein 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 *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
Azurin 4AZU *Type 1 copper protein
- mainly/3 sheet structure
Carbon monoxide dehydrogenase 1QJ2 Has active site Mo co-ordinated
(aerobic) by 1MCD (molybdopterin-
cytosine dinucleotide) and an
S-selenylcysteine. Associated with
proteins carrying Fe/S centres and
FAD. Feeds electrons into a
CO-insensitive respiratory chain
::;:;:::~:~:!~,:i, B I O E N E R G E T I C S 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
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
2CYP A b-type cytochrome from the
inter-membrane space of yeast
Cytochrome c550 1COT *Paracoccus denitrificans
D. lactate dehydrogenase 1FOX Peripheral membrane protein
from E. coli
DMSO (dimethylsulphoxide) 1CXS *Has active site Mo co-ordinated
reductase 1DMR by two MGD (molybdopterin-
4DMR guanosine dinucleotide)
1DMS molecules, each of which
1EU1 provides two sulfur ligands;
other ligands to Mo vary
Formate dehydrogenase 1KQF See Plate E
Fumarate reductase 1FUM See Plate E
1D4E *A flavo c-type cytochrome
enzyme from Shewanella
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

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 1QDB *Ammonia is reaction
hemes product. Unusual CXXCK heme
binding motif at active site
Nitrite reductase cytochrome cdl *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
1AOF From P. pantotrophus reduced
1QKS From P. pantotrophus oxidized
1NIR 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
Nitrous oxide reductase 1QNI *Contains both CUA site
1FWX 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
structure. From Pseudomonas
nautica and P. denitrificans
Pseudoazurin 3PAZ *Type 1 copper protein- mainly
8PAZ ]3 sheet structure. Oxidized and
reduced forms from Alcaligenes

Protein Code Comments

Rusticyanin 1A8Z *Type 1 Cu protein from

T. ferrooxidans
Sulfite oxidase 1SOX Chicken liver from inter-
mitochondrial space. Active site
Mo co-ordinated by a pterin
TMAO (Trimethylamine-N-oxide) 1TMO *From Shewanella massilia;
reductase has active site Mo co-ordinated
by two MGD groups
B. Photosynthetic proteins: (Chapter 6)
Bacteriorhodopsin 1C3W
Bacteria photosynthetic reaction centre 1PCR From R. sphaeroides
2PRC From R. viridis
Cytochrome-f 1HCZ Unusual c-type cytochrome with
/3-sheet structure
Halorhodopsin 1El2
LHCII Not deposited Spinach
LH2 1K2U Circular O~9/~9 structure
R. acidophilia
Photosystem 1 1JBO From S. elongatus
Photosystem 2 1FE1 From S. elongatus
Plastocyanin lAG6 From spinach
C. ATP synthase: (Chapter 7)
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
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