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1FRF
Asym. Unit
Info
Asym.Unit (136 KB)
Biol.Unit 1 (129 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS
Authors
:
Y. Montet, A. Volbeda, C. Piras, E. C. Hatchikian, M. Frey, J. C. Fonteci
Date
:
21 Jul 98 (Deposition) - 29 Jul 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : L,S
Biol. Unit 1: L,S (1x)
Keywords
:
Ni-Fe Hydrogenase, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Rousset, Y. Montet, B. Guigliarelli, N. Forget, M. Asso, P. Bertrand, J. C. Fontecilla-Camps, E. C. Hatchikian
3Fe-4S] To [4Fe-4S] Cluster Conversion In Desulfovibrio Fructosovorans [Nife] Hydrogenase By Site-Directed Mutagenesis
Proc. Natl. Acad. Sci. Usa V. 95 11625 1998
(for further references see the
PDB file header
)
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Hetero Components
(5, 6)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
2a: FE (III) ION (FEa)
3a: MAGNESIUM ION (MGa)
4a: NICKEL (II) ION (NIa)
5a: IRON/SULFUR CLUSTER (SF4a)
5b: IRON/SULFUR CLUSTER (SF4b)
View:
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Label:
No.
Name
Count
Type
Full Name
1
F3S
1
Ligand/Ion
FE3-S4 CLUSTER
2
FE
1
Ligand/Ion
FE (III) ION
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
NI
1
Ligand/Ion
NICKEL (II) ION
5
SF4
2
Ligand/Ion
IRON/SULFUR CLUSTER
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: ACT (AUTHOR)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS L:75 , CYS L:546 , NI L:566 , HOH L:616 , HOH L:622
BINDING SITE FOR RESIDUE FE L 565
2
AC2
SOFTWARE
CYS L:72 , CYS L:75 , CYS L:543 , CYS L:546 , FE L:565
BINDING SITE FOR RESIDUE NI L 566
3
AC3
SOFTWARE
GLU L:53 , GLU L:334 , GLN L:494 , LEU L:495 , HIS L:549 , HOH L:632
BINDING SITE FOR RESIDUE MG L 567
4
AC4
SOFTWARE
HIS S:184 , CYS S:187 , ARG S:189 , LEU S:190 , PHE S:193 , CYS S:212 , LEU S:213 , CYS S:218 , PRO S:221 , VAL S:239
BINDING SITE FOR RESIDUE SF4 S 265
5
AC5
SOFTWARE
LYS L:225 , GLN L:230 , THR S:223 , ASN S:225 , CYS S:227 , TRP S:237 , PRO S:238 , CYS S:245 , LEU S:246 , CYS S:248
BINDING SITE FOR RESIDUE F3S S 266
6
AC6
SOFTWARE
ARG L:70 , HIS L:228 , CYS S:17 , CYS S:20 , GLY S:112 , THR S:113 , CYS S:114 , GLY S:146 , CYS S:147 , PRO S:148
BINDING SITE FOR RESIDUE SF4 S 267
7
ACT
AUTHOR
NI L:566 , FE L:565
THE ACTIVE SITE CONTAINS TWO METALS: NI AND FE. THE NI ION IS COORDINATED BY TWO TERMINAL CYSTEINES CYS L 72 ? AND CYS L 543 ? AND TWO BRIDGING CYSTEINES BETWEEN FE AND NI, CYS L 75 ? AND CYS L 546 ?.
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (L:50-75)
2: NI_HGENASE_L_2 (L:540-549)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
NI_HGENASE_L_1
PS00507
Nickel-dependent hydrogenases large subunit signature 1.
PHNL_DESFR
50-75
1
L:50-75
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESFR
540-549
1
L:540-549
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 2)
Info
All SCOP Domains
1a: SCOP_d1frfs_ (S:)
2a: SCOP_d1frfl_ (L:)
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(
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)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
HydA/Nqo6-like
(51)
Superfamily
:
HydA/Nqo6-like
(51)
Family
:
Nickel-iron hydrogenase, small subunit
(39)
Protein domain
:
Nickel-iron hydrogenase, small subunit
(16)
Desulfovibrio fructosovorans [TaxId: 878]
(1)
1a
d1frfs_
S:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
Nickel-iron hydrogenase, large subunit
(17)
Desulfovibrio fructosovorans [TaxId: 878]
(1)
2a
d1frfl_
L:
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_1frfS01 (S:4-178)
2a: CATH_1frfS02 (S:179-263)
3a: CATH_1frfL00 (L:7-549)
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Homologous Superfamilies
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.700, no name defined]
(28)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
1a
1frfS01
S:4-178
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Cytochrome-c3 Hydrogenase; Chain A, domain 2
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain A, domain 2
(28)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
2a
1frfS02
S:179-263
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cytochrome-c3 Hydrogenase; chain B
(28)
Homologous Superfamily
:
Cytochrome-c3 Hydrogenase, chain B
(28)
Desulfovibrio fructosovorans. Organism_taxid: 878. Strain: wild type.
(5)
3a
1frfL00
L:7-549
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (136 KB)
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Header - Biol.Unit 1
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