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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 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
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
2CYP A b-type cytochrome from the
inter-membrane space of yeast
mitochondria
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
1QLA
1D4E *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 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
reduction
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
sites
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
seven-bladed/3-propeller
structure. From Pseudomonas
nautica and P. denitrificans
Pseudoazurin 3PAZ *Type 1 copper protein- mainly
8PAZ ]3 sheet structure. Oxidized and
reduced forms from Alcaligenes
faecalis
286 BIOENERGETICS3

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
7PCY
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
occupied
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