EzCatDB: T00030

DB codeT00030
RLCP classification10.22023.100.10525
10.23022.100.10580
10.22140.100.10551
CATH domainDomain 11.10.645.10Catalytic domain
Domain 23.40.50.700Catalytic domain
Domain 34.10.480.10Catalytic domain
E.C.1.12.2.1
CSA1h2r
MACiEM0126

CATH domainRelated DB codes (homologues)
1.10.645.10T00238
3.40.50.700T00238
4.10.480.10T00238

Enzyme Name
Swiss-protKEGG

P18188P12944P21852P18187P12943P21853
Protein namePeriplasmic [NiFe] hydrogenase large subunitPeriplasmic [NiFe] hydrogenase large subunitPeriplasmic [NiFe] hydrogenase large subunitPeriplasmic [NiFe] hydrogenase small subunitPeriplasmic [NiFe] hydrogenase small subunitPeriplasmic [NiFe] hydrogenase small subunitcytochrome-c3 hydrogenase
H2:ferricytochrome c3 oxidoreductase
cytochrome c3 reductase
cytochrome hydrogenase
hydrogenase [ambiguous]
SynonymsEC 1.12.2.1
NiFe hydrogenlyase large chain
EC 1.12.2.1
NiFe hydrogenlyase large chain
EC 1.12.2.1
NiFe hydrogenlyase large chain
EC 1.12.2.1
NiFe hydrogenlyase small chain
EC 1.12.2.1
NiFe hydrogenlyase small chain
EC 1.12.2.1
NiFe hydrogenlyase small chain


Swiss-prot:Accession NumberP18188P12944P21852P18187P12943P21853
Entry namePHNL_DESFRPHNL_DESGIPHNL_DESVMPHNS_DESFRPHNS_DESGIPHNS_DESVM
Activity2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3.2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3.2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3.2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3.2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3.2 H(2) + ferricytochrome c3 = 4 H(+) + ferrocytochrome c3.
SubunitHeterodimer of a large and a small subunit.Heterodimer of a large and a small subunit.Heterodimer of a large and a small subunit.Heterodimer of a large and a small subunit.Heterodimer of a large and a small subunit.Heterodimer of a large and a small subunit.
Subcellular locationPeriplasm.Periplasm.Periplasm.Periplasm.Periplasm.Periplasm.
CofactorBinds 1 nickel ion per subunit.Binds 1 nickel ion per subunit.Nickel.,Iron.Binds 2 4Fe-4S clusters.,Binds 1 3Fe-4S cluster.Binds 2 4Fe-4S clusters.,Binds 1 3Fe-4S cluster.Binds 2 4Fe-4S clusters.,Binds 1 3Fe-4S cluster.


CofactorsSubstratesProductsintermediates
KEGG-idL00024L00027L00028C00282C02682C00080C02684

Compound[4Fe-4S][3Fe-4S]Ni--Fe(CN)2(CO)H2ferricytochrome c3H+ferrocytochrome c3Transition-state Transition-state
Typeheavy metal,sulfide groupheavy metal,sulfide groupheavy metal,othersothersaromatic ring (with nitrogen atoms),carbohydrate,heavy metal,peptide/protein,sulfide groupothersaromatic ring (with nitrogen atoms),carbohydrate,heavy metal,peptide/protein,sulfide group

1frfLUnboundUnboundAnalogue:_NI-FeUnboundUnbound
Unbound

1yqwQUnboundUnboundBound:_NI-FCOUnboundUnbound
UnboundTransition-state-bound:PER(Ni-SU status)
1yqwRUnboundUnboundBound:_NI-FCOUnboundUnbound
UnboundTransition-state-bound:PER(Ni-SU status)
1yqwSUnboundUnboundBound:_NI-FCOUnboundUnbound
UnboundTransition-state-bound:PER(Ni-SU status)
1yrqHUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound

1yrqIUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound

1yrqJUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound

1yrqKUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound

1yrqMUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound

1yrqNUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound

1frvBUnboundUnboundAnalogue:_NI-FELUnboundUnbound
Unbound

1frvDUnboundUnboundAnalogue:_NI-FELUnboundUnbound
Unbound

1yq9HUnboundUnboundBound:_NI-FCOUnboundUnbound
UnboundTransition-state-bound:PER(Ni-A status)
1yq9IUnboundUnboundBound:_NI-FCOUnboundUnbound
UnboundTransition-state-bound:PER(Ni-A status)
2frvBUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound
Transition-state-bound:__O(Ni-B state)
2frvDUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound
Transition-state-bound:__O(Ni-B state)
2frvFUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound
Transition-state-bound:__O(Ni-B state)
2frvHUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound
Transition-state-bound:__O(Ni-B state)
2frvJUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound
Transition-state-bound:__O(Ni-B state)
2frvLUnboundUnboundBound:_NI-FCOUnboundUnbound
Unbound
Transition-state-bound:__O(Ni-B state)
1h2aLUnboundUnboundAnalogue:NFEUnboundUnbound
Unbound

1h2rLUnboundUnboundAnalogue:NFEUnboundUnbound
Unbound

1ubhLUnboundUnboundAnalogue:FNE-CMOUnboundUnbound
Unbound

1ubjLUnboundUnboundAnalogue:FNE-CMOUnboundUnbound
Unbound

1ubkLUnboundUnboundAnalogue:FNE-CMOUnboundUnbound
Unbound

1ublLUnboundUnboundAnalogue:FNE-CMOUnboundUnbound
Unbound

1ubmLUnboundUnboundAnalogue:FNEUnboundUnbound
Unbound

1uboLUnboundUnboundAnalogue:FNE-CMOUnboundUnbound
Unbound

1ubrLUnboundUnboundAnalogue:FNE-CMOUnboundUnbound
Unbound

1ubtLUnboundUnboundAnalogue:FNEUnboundUnbound
Unbound

1ubuLUnboundUnboundAnalogue:FNEUnboundUnbound
Unbound

1wuhLUnboundUnboundAnalogue:NFCUnboundUnbound
UnboundTransition-state-bound:NFC(Ni-A status)
1wuiLUnboundUnboundAnalogue:NFCUnboundUnbound
UnboundTransition-state-bound:NFC(Ni-A status)
1wujLUnboundUnboundAnalogue:NFOUnboundUnbound
Unbound
Transition-state-bound:NFO(Ni-B status)
1wukLUnboundUnboundAnalogue:NFOUnboundUnbound
Unbound
Transition-state-bound:NFO(oxidized status)
1wulLUnboundUnboundBound:NFRUnboundUnbound
Unbound

1frfS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yqwA01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yqwB01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yqwC01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yrqA01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yrqB01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yrqC01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yrqD01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yrqF01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yrqG01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1frvA01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1frvC01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yq9A01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1yq9B01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

2frvA01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

2frvC01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

2frvE01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

2frvG01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

2frvI01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

2frvS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1h2aS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1h2rS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1ubhS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1ubjS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1ubkS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1ublS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1ubmS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1uboS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1ubrS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1ubtS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1ubuS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1wuhS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1wuiS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1wujS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1wukS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1wulS01Bound:SF4UnboundUnboundUnboundUnbound
Unbound

1frfS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yqwA02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yqwB02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yqwC02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yrqA02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yrqB02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yrqC02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yrqD02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yrqF02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yrqG02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1frvA02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1frvC02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yq9A02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1yq9B02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

2frvA02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

2frvC02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

2frvE02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

2frvG02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

2frvI02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

2frvS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1h2aS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1h2rS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1ubhS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1ubjS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1ubkS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1ublS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1ubmS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1uboS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1ubrS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1ubtS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1ubuS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1wuhS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1wuiS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1wujS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1wukS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound

1wulS02Bound:SF4Bound:F3SUnboundUnboundUnbound
Unbound


Active-site residues
resource
literature [31], [32], [35], [37], [39], [45], [47]
pdbCatalytic residuesCofactor-binding residuesMain-chain involved in catalysis
1frfLGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yqwQGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yqwRGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yqwSGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yrqHGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yrqIGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yrqJGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yrqKGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yrqMGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1yrqNGLU 25;CYS 543
CYS 75;CYS 546(Fe and Nickel);CYS 72;CYS 543(Nickel)

1frvBGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

1frvDGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

1yq9HGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

1yq9IGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

2frvBGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

2frvDGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

2frvFGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

2frvHGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

2frvJGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

2frvLGLU 18;CYS 530
CYS 68;CYS 533(Fe and Nickel);CYS 65;CYS 530(Nickel)

1h2aLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1h2rLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1ubhLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1ubjLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1ubkLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1ublLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1ubmLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1uboLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1ubrLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1ubtLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1ubuLGLU 34;CYS 546
CYS 84;CYS 549(Fe and Nickel);CYS 81;CYS 546(Nickel)

1wuhLGLU 34;       
CSO 84;CYS 549(Fe and Nickel);CYS 81;CSO 546(Nickel)
CSO 84;CSO 546
1wuiLGLU 34;       
CSO 84;CYS 549(Fe and Nickel);CYS 81;CSO 546(Nickel)
CSO 84;CSO 546
1wujLGLU 34;       
CYS 84;CYS 549(Fe and Nickel);CYS 81;CSO 546(Nickel)
      ;CSO 546
1wukLGLU 34;       
CYS 84;CYS 549(Fe and Nickel);CYS 81;CSO 546(Nickel)
      ;CSO 546
1wulLGLU 34;       
CYS 84;CYS 549(Fe and Nickel);CYS 81;CSO 546(Nickel)
      ;CSO 546
1frfS01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yqwA01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yqwB01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yqwC01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yrqA01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yrqB01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yrqC01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yrqD01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yrqF01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1yrqG01THR 18
CYS 17;CYS 20;CYS 114;CYS 147(4Fe-4S cluster-1)

1frvA01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

1frvC01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

1yq9A01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

1yq9B01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

2frvA01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

2frvC01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

2frvE01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

2frvG01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

2frvI01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

2frvS01THR 18
CYS 17;CYS 20;CYS 112;CYS 148(4Fe-4S cluster-1)

1h2aS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1h2rS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1ubhS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1ubjS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1ubkS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1ublS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1ubmS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1uboS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1ubrS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1ubtS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1ubuS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1wuhS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1wuiS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1wujS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1wukS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1wulS01THR 18
CYS 17;CYS 20;CYS 114;CYS 150(4Fe-4S cluster-1)

1frfS02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yqwA02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yqwB02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yqwC02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yrqA02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yrqB02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yrqC02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yrqD02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yrqF02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1yrqG02
HIS 184;CYS 187;CYS 212;CYS 218(4Fe-4S cluster-2);CYS 227;CYS 245;CYS 248(3Fe-4S cluster)

1frvA02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

1frvC02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

1yq9A02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

1yq9B02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

2frvA02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

2frvC02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

2frvE02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

2frvG02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

2frvI02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

2frvS02
HIS 185;CYS 188;CYS 213;CYS 219(4Fe-4S cluster-2);CYS 228;CYS 246;CYS 249(3Fe-4S cluster)

1h2aS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1h2rS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1ubhS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1ubjS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1ubkS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1ublS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1ubmS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1uboS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1ubrS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1ubtS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1ubuS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1wuhS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1wuiS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1wujS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1wukS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)

1wulS02
HIS 188;CYS 191;CYS 216;CYS 222(4Fe-4S cluster-2);CYS 231;CYS 249;CYS 252(3Fe-4S cluster)


References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]p.987-988
[9]Fig.5, Fig.9, Fig.10, p.14346-14348
[10]p.825-828
[12]Fig.5, p.582-585
[14]Fig.7, p.12995-12996
[16]Fig.4, p.7850-7854
[17]Fig.2, p.664-665
[20]p.1675-1677
[21]p.399-400
[22]p.11628-11630
[23]p.298
[24]p.3336-3337
[25]Fig.3, p.553-554
[31]Scheme 1, Fig.2, p.6202-6203
[32]Scheme 1, p.58402
[33]Table 1, p.469-472
[34]p.457-458
[35]p.71-73, p.77-80
[36]p.156-157, p.158-159
[37]Fig.4, p.4432-4434
[38]Fig.7, p.11634-11635
[42]Fig.8, p.92
[44]Fig.2, p.134-138
[45]p.10511-10513
[47]Fig.1, p.641-642
[48]Fig3., Fig.4, p.872-875
[50]Fig.6, p.246-248
[51]Fig.3, p.1637-1640

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TitlePurification and properties of the soluble hydrogenase from Desulfovibrio desulfuricans (strain Norway 4).
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TitleAnalysis of the active center of hydrogenase from Desulfovibrio vulgaris Miyazaki by magnetic measurements.
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Pages635-43
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Related Swiss-protP18187,P18188
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PubMed ID1316088
JournalAnal Chem
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Volume64
Pages641-6
AuthorsParpaleix T, Laval JM, Majda M, Bourdillon C
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PubMed ID1558764
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Pages109-35
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TitleStructure-function relationships among the nickel-containing hydrogenases.
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PubMed ID8399280
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Year1993
Volume1144
Pages302-8
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TitleCharacterization of D. desulfuricans (ATCC 27774) [NiFe] hydrogenase EPR and redox properties of the native and the dihydrogen reacted states.
[7]
PubMed ID8223656
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Pages981-9
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TitleVoltammetric studies of the catalytic electron-transfer process between the Desulfovibrio gigas hydrogenase and small proteins isolated from the same genus.
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PubMed ID8501043
JournalJ Bacteriol
Year1993
Volume175
Pages3388-93
AuthorsRousset M, Dermoun Z, Wall JD, Belaich JP
TitleAnalysis of the periplasmic [NiFe] hydrogenase transcription unit from Desulfovibrio fructosovorans.
[9]
PubMed ID7947844
JournalBiochemistry
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Volume33
Pages14339-50
AuthorsRoberts LM, Lindahl PA
TitleAnalysis of oxidative titrations of Desulfovibrio gigas hydrogenase; implications for the catalytic mechanism.
[10]
PubMed ID8174562
JournalEur J Biochem
Year1994
Volume221
Pages821-9
AuthorsVerhagen MF, Wolbert RB, Hagen WR
TitleCytochrome c553 from Desulfovibrio vulgaris (Hildenborough). Electrochemical properties and electron transfer with hydrogenase.
[11]
PubMed ID7718585
JournalBiochemistry
Year1995
Volume34
Pages4781-90
AuthorsGuigliarelli B, More C, Fournel A, Asso M, Hatchikian EC, Williams R, Cammack R, Bertrand P
TitleStructural organization of the Ni and (4Fe-4S) centers in the active form of Desulfovibrio gigas hydrogenase. Analysis of the magnetic interactions by electron paramagnetic resonance spectroscopy.
[12]
CommentsX-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS).
PubMed ID7854413
JournalNature
Year1995
Volume373
Pages580-7
AuthorsVolbeda A, Charon MH, Piras C, Hatchikian EC, Frey M, Fontecilla-Camps JC
TitleCrystal structure of the nickel-iron hydrogenase from Desulfovibrio gigas.
Related PDB1frv
Related Swiss-protP12943,P12944
[13]
PubMed ID8973216
JournalBiochemistry
Year1996
Volume35
Pages16399-406
AuthorsDole F, Medina M, More C, Cammack R, Bertrand P, Guigliarelli B
TitleSpin-spin interactions between the Ni site and the [4Fe-4S] centers as a probe of light-induced structural changes in active Desulfovibrio gigas hydrogenase.
[14]
CommentsX-ray crystallography
JournalJ Am Chem Soc
Year1996
Volume118
Pages12989-96
AuthorsVolbeda A, Garcin E, Piras C, de Lacey A L, Fernandez VM, Hatchikian EC, Frey M, Fontecilla-Camps JC
TitleStructure of the [NiFe] Hydrogenase Active Site: Evidence for Biologically Uncommon Fe Ligands.
Related PDB2frv
[15]
PubMed ID8605619
JournalNat Struct Biol
Year1996
Volume3
Pages213-7
AuthorsCollman JP
TitleCoupling H2 to electron transfer.
[16]
PubMed ID9201928
JournalBiochemistry
Year1997
Volume36
Pages7847-54
AuthorsDole F, Fournel A, Magro V, Hatchikian EC, Bertrand P, Guigliarelli B
TitleNature and electronic structure of the Ni-X dinuclear center of Desulfovibrio gigas hydrogenase. Implications for the enzymatic mechanism.
[17]
PubMed ID9479448
JournalBiochimie
Year1997
Volume79
Pages661-6
AuthorsFontecilla-Camps JC, Frey M, Garcin E, Hatchikian C, Montet Y, Piras C, Vernede X, Volbeda A
TitleHydrogenase: a hydrogen-metabolizing enzyme. What do the crystal structures tell us about its mode of action?
[18]
PubMed ID9228943
JournalNat Struct Biol
Year1997
Volume4
Pages523-6
AuthorsMontet Y, Amara P, Volbeda A, Vernede X, Hatchikian EC, Field MJ, Frey M, Fontecilla-Camps JC
TitleGas access to the active site of Ni-Fe hydrogenases probed by X-ray crystallography and molecular dynamics.
[19]
PubMed ID8990114
JournalNature
Year1997
Volume385
Pages126
AuthorsHappe RP, Roseboom W, Pierik AJ, Albracht SP, Bagley KA
TitleBiological activation of hydrogen.
[20]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS) OF 19-552.
PubMed ID9438867
JournalStructure
Year1997
Volume5
Pages1671-80
AuthorsHiguchi Y, Yagi T, Yasuoka N
TitleUnusual ligand structure in Ni-Fe active center and an additional Mg site in hydrogenase revealed by high resolution X-ray structure analysis.
Related PDB1h2a
Related Swiss-protP21852,P21853
[21]
PubMed ID9765886
JournalBiochem Soc Trans
Year1998
Volume26
Pages396-401
AuthorsGarcin E, Montet Y, Volbeda A, Hatchikian C, Frey M, Fontecilla-Camps JC
TitleStructural bases for the catalytic mechanism of [NiFe] hydrogenases.
[22]
CommentsX-ray Diffraction
PubMed ID9751716
JournalProc Natl Acad Sci U S A
Year1998
Volume95
Pages11625-30
AuthorsRousset M, Montet Y, Guigliarelli B, Forget N, Asso M, Bertrand P, Fontecilla-Camps JC, Hatchikian EC
Title[3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis.
Related PDB1frf
[23]
PubMed ID10049702
JournalBiochem Biophys Res Commun
Year1999
Volume255
Pages295-9
AuthorsHiguchi Y, Yagi T
TitleLiberation of hydrogen sulfide during the catalytic action of Desulfovibrio hydrogenase under the atmosphere of hydrogen.
[24]
PubMed ID9920874
JournalJ Biol Chem
Year1999
Volume274
Pages3331-7
AuthorsPierik AJ, Roseboom W, Happe RP, Bagley KA, Albracht SP
TitleCarbon monoxide and cyanide as intrinsic ligands to iron in the active site of [NiFe]-hydrogenases. NiFe(CN)2CO, Biology's way to activate H2.
[25]
CommentsX-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS).
PubMed ID10378274
JournalStructure Fold Des
Year1999
Volume7
Pages549-56
AuthorsHiguchi Y, Ogata H, Miki K, Yasuoka N, Yagi T
TitleRemoval of the bridging ligand atom at the Ni-Fe active site of [NiFe] hydrogenase upon reduction with H2, as revealed by X-ray structure analysis at 1.4 A resolution.
Related PDB1h2r
Related Swiss-protP21852,P21853
[26]
PubMed ID11128995
JournalJ Biol Inorg Chem
Year2000
Volume5
Pages682-91
AuthorsBertrand P, Dole F, Asso M, Guigliarelli B
TitleIs there a rate-limiting step in the catalytic cycle of Ni-Fe hydrogenases?
[27]
PubMed ID10766434
JournalJ Biol Inorg Chem
Year2000
Volume5
Pages36-44
AuthorsTrofanchuk O, Stein M, Gessner C, Lendzian F, Higuchi Y, Lubitz W
TitleSingle crystal EPR studies of the oxidized active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.
[28]
PubMed ID11001090
JournalJ Inorg Biochem
Year2000
Volume80
Pages205-11
AuthorsHiguchi Y, Toujou F, Tsukamoto K, Yagi T
TitleThe presence of a SO molecule in [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki as detected by mass spectrometry.
[29]
PubMed ID11170458
JournalBiochemistry
Year2001
Volume40
Pages1317-24
AuthorsFritz G, Griesshaber D, Seth O, Kroneck PM
TitleNonaheme cytochrome c, a new physiological electron acceptor for [Ni,Fe] hydrogenase in the sulfate-reducing bacterium Desulfovibrio desulfuricans Essex: primary sequence, molecular parameters, and redox properties.
[30]
PubMed ID11195380
JournalInorg Chem
Year2001
Volume40
Pages18-24
AuthorsLi S, Hall MB
TitleModeling the active sites of metalloenzymes. 4. Predictions of the unready states of [NiFe] Desulfovibrio gigas hydrogenase from density functional theory.
[31]
PubMed ID11703120
JournalInorg Chem
Year2001
Volume40
Pages6201-3
AuthorsNiu S, Hall MB
TitleModeling the active sites in metalloenzymes 5. The heterolytic bond cleavage of H(2) in the [NiFe] hydrogenase of desulfovibrio gigas by a nucleophilic addition mechanism.
[32]
PubMed ID11403633
JournalJ Am Chem Soc
Year2001
Volume123
Pages5839-40
AuthorsStein M, van Lenthe E, Baerends EJ, Lubitz W
TitleRelativistic DFT calculations of the paramagnetic intermediates of [NiFe] hydrogenase. Implications for the enzymatic mechanism.
[33]
PubMed ID11372206
JournalJ Biol Inorg Chem
Year2001
Volume6
Pages467-73
AuthorsFan HJ, Hall MB
TitleRecent theoretical predictions of the active site for the observed forms in the catalytic cycle of Ni-Fe hydrogenase.
[34]
PubMed ID11372204
JournalJ Biol Inorg Chem
Year2001
Volume6
Pages453-9
AuthorsMaroney MJ, Bryngelson PA
TitleSpectroscopic and model studies of the Ni-Fe hydrogenase reaction mechanism.
[35]
PubMed ID11191224
JournalJ Biol Inorg Chem
Year2001
Volume6
Pages63-81
AuthorsMatias PM, Soares CM, Saraiva LM, Coelho R, Morais J, Le Gall J, Carrondo MA
Title[NiFe] hydrogenase from Desulfovibrio desulfuricans ATCC 27774: gene sequencing, three-dimensional structure determination and refinement at 1.8 A and modelling studies of its interaction with the tetrahaem cytochrome c3.
[36]
PubMed ID11921392
JournalChembiochem
Year2002
Volume3
Pages153-60
AuthorsFrey M
TitleHydrogenases: hydrogen-activating enzymes.
[37]
PubMed ID12184759
JournalInorg Chem
Year2002
Volume41
Pages4424-34
AuthorsStadler C, de Lacey AL, Montet Y, Volbeda A, Fontecilla-Camps JC, Conesa JC, Fernandez VM
TitleDensity functional calculations for modeling the active site of nickel-iron hydrogenases. 2. Predictions for the unready and ready States and the corresponding activation processes.
[38]
PubMed ID11782180
JournalJ Am Chem Soc
Year2002
Volume124
Pages281-6
AuthorsCarepo M, Tierney DL, Brondino CD, Yang TC, Pamplona A, Telser J, Moura I, Moura JJ, Hoffman BM
Title17O ENDOR detection of a solvent-derived Ni-(OH(x))-Fe bridge that is lost upon activation of the hydrogenase from Desulfovibrio gigas.
[39]
CommentsX-ray Diffraction
PubMed ID12296727
JournalJ Am Chem Soc
Year2002
Volume124
Pages11628-35
AuthorsOgata H, Mizoguchi Y, Mizuno N, Miki K, Adachi S, Yasuoka N, Yagi T, Yamauchi O, Hirota S, Higuchi Y
TitleStructural studies of the carbon monoxide complex of [NiFe]hydrogenase from Desulfovibrio vulgaris Miyazaki F: suggestion for the initial activation site for dihydrogen.
Related PDB1ubh,1ubj,1ubk,1ubl,1ubm,1ubo,1ubr,1ubt
[40]
PubMed ID11935356
JournalJ Biol Inorg Chem
Year2002
Volume7
Pages318-26
AuthorsDe Lacey AL, Stadler C, Fernandez VM, Hatchikian EC, Fan HJ, Li S, Hall MB
TitleIR spectroelectrochemical study of the binding of carbon monoxide to the active site of Desulfovibrio fructosovorans Ni-Fe hydrogenase.
[41]
PubMed ID11862554
JournalJ Biol Inorg Chem
Year2002
Volume7
Pages177-94
AuthorsMuller A, Tscherny I, Kappl R, Hatchikian C, Huttermann J, Cammack R
TitleHydrogenases in the "active" state: determination of g-matrix axes and electron spin distribution at the active site by 1H ENDOR spectroscopy.
[42]
PubMed ID12515509
JournalJ Am Chem Soc
Year2003
Volume125
Pages
AuthorsFoerster S, Stein M, Brecht M, Ogata H, Higuchi Y, Lubitz W
TitleSingle crystal EPR studies of the reduced active site of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F.
[43]
PubMed ID12459907
JournalJ Biol Inorg Chem
Year2003
Volume8
Pages129-34
AuthorsDeLacey AL, Fernandez VM, Rousset M, Cavazza C, Hatchikian EC
TitleSpectroscopic and kinetic characterization of active site mutants of Desulfovibrio fructosovoransNi-Fe hydrogenase.
[44]
PubMed ID15062773
JournalCurr Opin Chem Biol
Year2004
Volume8
Pages133-40
AuthorsArmstrong FA
TitleHydrogenases: active site puzzles and progress.
[45]
PubMed ID14688251
JournalJ Biol Chem
Year2004
Volume279
Pages10508-13
AuthorsDementin S, Burlat B, De Lacey AL, Pardo A, Adryanczyk-Perrier G, Guigliarelli B, Fernandez VM, Rousset M
TitleA glutamate is the essential proton transfer gate during the catalytic cycle of the [NiFe] hydrogenase.
[46]
PubMed ID15365900
JournalJ Biol Inorg Chem
Year2004
Volume9
Pages873-84
AuthorsBruschi M, De Gioia L, Zampella G, Reiher M, Fantucci P, Stein M
TitleA theoretical study of spin states in Ni-S4 complexes and models of the [NiFe] hydrogenase active site.
[47]
PubMed ID15175937
JournalJ Biol Inorg Chem
Year2004
Volume9
Pages636-42
AuthorsDe Lacey AL, Pardo A, Fernandez VM, Dementin S, Adryanczyk-Perrier G, Hatchikian EC, Rousset M
TitleFTIR spectroelectrochemical study of the activation and inactivation processes of [NiFe] hydrogenases: effects of solvent isotope replacement and site-directed mutagenesis.
[48]
PubMed ID15134933
JournalJ Inorg Biochem
Year2004
Volume98
Pages862-77
AuthorsStein M, Lubitz W
TitleRelativistic DFT calculation of the reaction cycle intermediates of [NiFe] hydrogenase: a contribution to understanding the enzymatic mechanism.
[49]
PubMed ID15667250
JournalBiochem Soc Trans
Year2005
Volume33
Pages7-11
Authorsvan Gastel M, Fichtner C, Neese F, Lubitz W
TitleEPR experiments to elucidate the structure of the ready and unready states of the [NiFe] hydrogenase of Desulfovibrio vulgaris Miyazaki F.
[50]
PubMed ID15803334
JournalJ Biol Inorg Chem
Year2005
Volume10
Pages239-49
AuthorsVolbeda A, Martin L, Cavazza C, Matho M, Faber BW, Roseboom W, Albracht SP, Garcin E, Rousset M, Fontecilla-Camps JC
TitleStructural differences between the ready and unready oxidized states of [NiFe] hydrogenases.
Related PDB1yq9,1yqw,1yrq
[51]
PubMed ID16271886
JournalStructure
Year2005
Volume13
Pages1635-42
AuthorsOgata H, Hirota S, Nakahara A, Komori H, Shibata N, Kato T, Kano K, Higuchi Y
TitleActivation process of [NiFe] hydrogenase elucidated by high-resolution X-Ray analyses: conversion of the ready to the unready state.
Related PDB1wuh,1wui,1wuj,1wuk,1wul

comments
This enzyme catalyzes the following reactions:
(A) Electron transfer from heme iron of cytochrome c3 to [4Fe-4S] cluster-2 located on the surface of small subunit:
(A1) His184 (1frf) bound to Fe4-S4, is exposed to the surface of the S subunit. This residue might interact with cytochrome c3, for electron transfer (see [12]).
(B) Electron transfer from [4Fe-4S] cluster-2 to [3Fe-4S] cluster:
(B1) Indirect transfer from [4Fe-4S] cluster-2 to [3Fe-4S] cluster through Cys218 (bound to [4Fe-4S] cluster-2) and Cys245 (bound to [3Fe-4S]) (see [12]).
(C) Electron transfer from [3Fe-4S] cluster to [4Fe-4S] cluster-1:
(C1) Indirect transfer from [3Fe-4S] cluster to [4Fe-4S] cluster-1 through Cys248 (bound to [3Fe-4S]) and Cys147 (bound to [4Fe-4S] cluster-1) (see [12]).
(D) Electron transfer from [4Fe-4S] cluster-1 to the Nickel-Iron cluster (reaction center):
(D1) Indirect transfer from [4Fe-4S] cluster-1 to Nickel-Iron cluster through Cys17 (bound to [4Fe-4S] cluster-1) and Cys72 of Large subunit (bound to Nickel-Iron cluster) (see [12]).
(E) Hydrogenation at the Nickel-Iron cluster (reaction center):

createdupdated
2005-08-122009-02-26
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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