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3H3X
Asym. Unit
Info
Asym.Unit (392 KB)
Biol.Unit 1 (132 KB)
Biol.Unit 2 (132 KB)
Biol.Unit 3 (131 KB)
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(1)
Title
:
STRUCTURE OF THE V74M LARGE SUBUNIT MUTANT OF NI-FE HYDROGENASE IN AN OXIDIZED STATE
Authors
:
A. Volbeda, N. Martinez, L. Martin, J. C. Fontecilla-Camps
Date
:
17 Apr 09 (Deposition) - 21 Jul 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B,C,Q,R,S
Biol. Unit 1: A,Q (1x)
Biol. Unit 2: B,R (1x)
Biol. Unit 3: C,S (1x)
Keywords
:
Ni-Fe Hydrogenase Tunnel Mutant, Nickel, Iron, Oxidoreductase, Iron- Sulfur, Metal-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Dementin, F. Leroux, L. Cournac, A. L. De Lacey, A. Volbeda, C. Leger, B. Burlat, N. Martinez, S. Champ, L. Martin, O. Sanganas, M. Haumann, V. M. Fernandez, B. Guigliarelli, J. C. Fontecilla-Camps M. Rousset
Introduction Of Methionines In The Gas Channel Makes [Nife] Hydrogenase Aero-Tolerant
J. Am. Chem. Soc. V. 131 10156 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(6, 25)
Info
All Hetero Components
1a: FE3-S4 CLUSTER (F3Sa)
1b: FE3-S4 CLUSTER (F3Sb)
1c: FE3-S4 CLUSTER (F3Sc)
2a: CARBONMONOXIDE-(DICYANO) IRON (FCOa)
2b: CARBONMONOXIDE-(DICYANO) IRON (FCOb)
2c: CARBONMONOXIDE-(DICYANO) IRON (FCOc)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
3d: GLYCEROL (GOLd)
3e: GLYCEROL (GOLe)
3f: GLYCEROL (GOLf)
3g: GLYCEROL (GOLg)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
5a: NICKEL (II) ION (NIa)
5b: NICKEL (II) ION (NIb)
5c: NICKEL (II) ION (NIc)
6a: IRON/SULFUR CLUSTER (SF4a)
6b: IRON/SULFUR CLUSTER (SF4b)
6c: IRON/SULFUR CLUSTER (SF4c)
6d: IRON/SULFUR CLUSTER (SF4d)
6e: IRON/SULFUR CLUSTER (SF4e)
6f: IRON/SULFUR CLUSTER (SF4f)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
F3S
3
Ligand/Ion
FE3-S4 CLUSTER
2
FCO
3
Ligand/Ion
CARBONMONOXIDE-(DICYANO) IRON
3
GOL
7
Ligand/Ion
GLYCEROL
4
MG
3
Ligand/Ion
MAGNESIUM ION
5
NI
3
Ligand/Ion
NICKEL (II) ION
6
SF4
6
Ligand/Ion
IRON/SULFUR CLUSTER
[
close Hetero Component info
]
Sites
(25, 25)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:184 , CYS A:187 , ARG A:189 , LEU A:190 , PHE A:193 , CYS A:212 , LEU A:213 , TYR A:214 , CYS A:218
BINDING SITE FOR RESIDUE SF4 A 265
02
AC2
SOFTWARE
ASN A:225 , CYS A:227 , PHE A:232 , TRP A:237 , CYS A:245 , LEU A:246 , CYS A:248 , LYS Q:225 , GLN Q:230
BINDING SITE FOR RESIDUE F3S A 266
03
AC3
SOFTWARE
GLU A:16 , CYS A:17 , CYS A:20 , THR A:113 , CYS A:114 , GLY A:146 , CYS A:147 , PRO A:148 , ARG Q:70 , HIS Q:228
BINDING SITE FOR RESIDUE SF4 A 267
04
AC4
SOFTWARE
ASP A:168 , LEU A:169 , LYS A:176 , HOH A:322
BINDING SITE FOR RESIDUE GOL A 271
05
AC5
SOFTWARE
CYS Q:75 , VAL Q:78 , HIS Q:79 , ALA Q:474 , PRO Q:475 , ARG Q:476 , VAL Q:497 , PRO Q:498 , SER Q:499 , CYS Q:546 , NI Q:551
BINDING SITE FOR RESIDUE FCO Q 550
06
AC6
SOFTWARE
CYS Q:72 , CYS Q:75 , CYS Q:543 , CYS Q:546 , FCO Q:550
BINDING SITE FOR RESIDUE NI Q 551
07
AC7
SOFTWARE
GLU Q:53 , LEU Q:495 , HIS Q:549 , HOH Q:554 , HOH Q:555 , HOH Q:556
BINDING SITE FOR RESIDUE MG Q 553
08
AC8
SOFTWARE
ARG Q:100 , ASN Q:104 , PHE Q:295 , ALA Q:296 , THR Q:297 , TRP Q:442 , GLU Q:445
BINDING SITE FOR RESIDUE GOL Q 561
09
AC9
SOFTWARE
PHE C:198 , ASN Q:181 , ALA Q:182 , LEU Q:185 , ARG Q:529
BINDING SITE FOR RESIDUE GOL Q 562
10
BC1
SOFTWARE
HIS B:184 , CYS B:187 , ARG B:189 , LEU B:190 , CYS B:212 , LEU B:213 , TYR B:214 , CYS B:218 , PRO B:221
BINDING SITE FOR RESIDUE SF4 B 265
11
BC2
SOFTWARE
ASN B:225 , CYS B:227 , PHE B:232 , TRP B:237 , PRO B:238 , CYS B:245 , LEU B:246 , CYS B:248 , GLN R:230
BINDING SITE FOR RESIDUE F3S B 266
12
BC3
SOFTWARE
GLU B:16 , CYS B:17 , CYS B:20 , GLY B:112 , THR B:113 , CYS B:114 , GLY B:146 , CYS B:147 , PRO B:148 , HOH B:269 , ARG R:70
BINDING SITE FOR RESIDUE SF4 B 267
13
BC4
SOFTWARE
CYS R:75 , HIS R:79 , ALA R:474 , PRO R:475 , ARG R:476 , LEU R:479 , VAL R:497 , PRO R:498 , SER R:499 , CYS R:546 , NI R:551
BINDING SITE FOR RESIDUE FCO R 550
14
BC5
SOFTWARE
CYS R:72 , CYS R:75 , CYS R:543 , CYS R:546 , FCO R:550
BINDING SITE FOR RESIDUE NI R 551
15
BC6
SOFTWARE
GLU R:53 , LEU R:495 , HIS R:549 , HOH R:554 , HOH R:555 , HOH R:556
BINDING SITE FOR RESIDUE MG R 553
16
BC7
SOFTWARE
ALA B:55 , ASN R:181 , ALA R:182 , TYR R:183 , LEU R:185 , ARG R:529 , HOH R:670
BINDING SITE FOR RESIDUE GOL R 561
17
BC8
SOFTWARE
THR R:286 , SER R:287 , ASN R:288 , PRO R:514 , HOH R:630
BINDING SITE FOR RESIDUE GOL R 562
18
BC9
SOFTWARE
ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , GLN R:310 , GLU R:445 , HOH R:641
BINDING SITE FOR RESIDUE GOL R 563
19
CC1
SOFTWARE
HIS C:184 , CYS C:187 , LEU C:190 , CYS C:212 , LEU C:213 , CYS C:218 , PRO C:221
BINDING SITE FOR RESIDUE SF4 C 265
20
CC2
SOFTWARE
ASN C:225 , CYS C:227 , PHE C:232 , TRP C:237 , CYS C:245 , LEU C:246 , CYS C:248 , GLN S:230
BINDING SITE FOR RESIDUE F3S C 266
21
CC3
SOFTWARE
GLU C:16 , CYS C:17 , CYS C:20 , THR C:113 , CYS C:114 , GLY C:146 , CYS C:147 , ARG S:70
BINDING SITE FOR RESIDUE SF4 C 267
22
CC4
SOFTWARE
CYS S:75 , VAL S:78 , HIS S:79 , ALA S:474 , PRO S:475 , ARG S:476 , LEU S:479 , VAL S:497 , PRO S:498 , SER S:499 , CYS S:546 , NI S:551
BINDING SITE FOR RESIDUE FCO S 550
23
CC5
SOFTWARE
CYS S:72 , CYS S:75 , CYS S:543 , CYS S:546 , FCO S:550
BINDING SITE FOR RESIDUE NI S 551
24
CC6
SOFTWARE
GLU S:53 , LEU S:495 , HIS S:549 , HOH S:554 , HOH S:555 , HOH S:556
BINDING SITE FOR RESIDUE MG S 553
25
CC7
SOFTWARE
ARG S:100 , ASN S:104 , PHE S:295 , ALA S:296 , THR S:297 , TRP S:442 , GLU S:445
BINDING SITE FOR RESIDUE GOL S 561
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
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Sorry, no Info available
[
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PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: NI_HGENASE_L_1 (Q:50-75,R:50-75,S:50-75)
2: NI_HGENASE_L_2 (Q:540-549,R:540-549,S:540-549)
;
View:
Select:
Label:
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
3
Q:50-75
R:50-75
S:50-75
2
NI_HGENASE_L_2
PS00508
Nickel-dependent hydrogenases large subunit signature 2.
PHNL_DESFR
540-549
3
Q:540-549
R:540-549
S:540-549
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 6)
Info
All SCOP Domains
1a: SCOP_d3h3xa_ (A:)
1b: SCOP_d3h3xb_ (B:)
1c: SCOP_d3h3xc_ (C:)
2a: SCOP_d3h3xq_ (Q:)
2b: SCOP_d3h3xr_ (R:)
2c: SCOP_d3h3xs_ (S:)
View:
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Classes
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)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
automated matches
(23)
Desulfovibrio fructosovorans [TaxId: 878]
(5)
1a
d3h3xa_
A:
1b
d3h3xb_
B:
1c
d3h3xc_
C:
Fold
:
HydB/Nqo4-like
(55)
Superfamily
:
HydB/Nqo4-like
(55)
Family
:
Nickel-iron hydrogenase, large subunit
(40)
Protein domain
:
automated matches
(23)
Desulfovibrio fructosovorans [TaxId: 878]
(5)
2a
d3h3xq_
Q:
2b
d3h3xr_
R:
2c
d3h3xs_
S:
[
close SCOP info
]
CATH Domains
(3, 9)
Info
all CATH domains
1a: CATH_3h3xA01 (A:3-178)
1b: CATH_3h3xB01 (B:3-178)
1c: CATH_3h3xC01 (C:5-178)
2a: CATH_3h3xA02 (A:179-263)
2b: CATH_3h3xB02 (B:179-263)
2c: CATH_3h3xC02 (C:179-263)
3a: CATH_3h3xQ00 (Q:6-549)
3b: CATH_3h3xS00 (S:6-549)
3c: CATH_3h3xR00 (R:5-549)
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)
(
)
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)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
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: dsm 3604.
(1)
1a
3h3xA01
A:3-178
1b
3h3xB01
B:3-178
1c
3h3xC01
C:5-178
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: dsm 3604.
(1)
2a
3h3xA02
A:179-263
2b
3h3xB02
B:179-263
2c
3h3xC02
C: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: dsm 3604.
(1)
3a
3h3xQ00
Q:6-549
3b
3h3xS00
S:6-549
3c
3h3xR00
R:5-549
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asym.Unit (392 KB)
Header - Asym.Unit
Biol.Unit 1 (132 KB)
Header - Biol.Unit 1
Biol.Unit 2 (132 KB)
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Biol.Unit 3 (131 KB)
Header - Biol.Unit 3
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