4UEQ | pdb_00004ueq

Structure of the V74C large subunit mutant of D. fructosovorans NiFe- hydrogenase


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ad4ueqa_ Multi-domain proteins (alpha and beta) HydA/Nqo6-like HydA/Nqo6-like Nickel-iron hydrogenase, small subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
Bd4ueqb_ Multi-domain proteins (alpha and beta) HydA/Nqo6-like HydA/Nqo6-like Nickel-iron hydrogenase, small subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
Cd4ueqc_ Multi-domain proteins (alpha and beta) HydA/Nqo6-like HydA/Nqo6-like Nickel-iron hydrogenase, small subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
Dd4ueqd_ Multi-domain proteins (alpha and beta) HydA/Nqo6-like HydA/Nqo6-like Nickel-iron hydrogenase, small subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
Ed4ueqe_ Multi-domain proteins (alpha and beta) HydA/Nqo6-like HydA/Nqo6-like Nickel-iron hydrogenase, small subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
Fd4ueqf_ Multi-domain proteins (alpha and beta) HydA/Nqo6-like HydA/Nqo6-like Nickel-iron hydrogenase, small subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
G [auth Q]d4ueqq_ Multi-domain proteins (alpha and beta) HydB/Nqo4-like HydB/Nqo4-like Nickel-iron hydrogenase, large subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
H [auth R]d4ueqr_ Multi-domain proteins (alpha and beta) HydB/Nqo4-like HydB/Nqo4-like Nickel-iron hydrogenase, large subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
I [auth S]d4ueqs_ Multi-domain proteins (alpha and beta) HydB/Nqo4-like HydB/Nqo4-like Nickel-iron hydrogenase, large subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
J [auth T]d4ueqt_ Multi-domain proteins (alpha and beta) HydB/Nqo4-like HydB/Nqo4-like Nickel-iron hydrogenase, large subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
K [auth U]d4uequ_ Multi-domain proteins (alpha and beta) HydB/Nqo4-like HydB/Nqo4-like Nickel-iron hydrogenase, large subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)
L [auth V]d4ueqv_ Multi-domain proteins (alpha and beta) HydB/Nqo4-like HydB/Nqo4-like Nickel-iron hydrogenase, large subunit automated matches (Solidesulfovibrio fructosivorans JJ] ) [TaxId: 596151 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
AOxidored_q6e4ueqA1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
ANiFe_hyd_SSU_Ce4ueqA2 A: few secondary structure elementsX: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunitF: NiFe_hyd_SSU_CECOD (1.6)
BOxidored_q6e4ueqB2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
BNiFe_hyd_SSU_Ce4ueqB1 A: few secondary structure elementsX: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunitF: NiFe_hyd_SSU_CECOD (1.6)
COxidored_q6e4ueqC2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
CNiFe_hyd_SSU_Ce4ueqC1 A: few secondary structure elementsX: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunitF: NiFe_hyd_SSU_CECOD (1.6)
DOxidored_q6e4ueqD2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
DNiFe_hyd_SSU_Ce4ueqD1 A: few secondary structure elementsX: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunitF: NiFe_hyd_SSU_CECOD (1.6)
EOxidored_q6e4ueqE1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
ENiFe_hyd_SSU_Ce4ueqE2 A: few secondary structure elementsX: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunitF: NiFe_hyd_SSU_CECOD (1.6)
FOxidored_q6e4ueqF2 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Class I glutamine amidotransferase-likeT: CheY-likeF: Oxidored_q6ECOD (1.6)
FNiFe_hyd_SSU_Ce4ueqF1 A: few secondary structure elementsX: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)H: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunit (From Topology)T: Fe-S cluster-binding domain in nickel-iron hydrogenase small subunitF: NiFe_hyd_SSU_CECOD (1.6)
G [auth Q]NiFeSe_Hases_2nde4ueqQ1 A: beta meandersX: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)T: all-beta domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_2ndECOD (1.6)
G [auth Q]NiFeSe_Hases_1ste4ueqQ2 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: NiFeSe_Hases_1stECOD (1.6)
G [auth Q]NiFeSe_Hases_3rde4ueqQ4 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rdECOD (1.6)
G [auth Q]NiFeSe_Hases_3rd_1e4ueqQ3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)
H [auth R]NiFeSe_Hases_2nde4ueqR3 A: beta meandersX: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)T: all-beta domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_2ndECOD (1.6)
H [auth R]NiFeSe_Hases_1ste4ueqR2 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: NiFeSe_Hases_1stECOD (1.6)
H [auth R]NiFeSe_Hases_3rde4ueqR1 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rdECOD (1.6)
H [auth R]NiFeSe_Hases_3rd_1e4ueqR4 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)
I [auth S]NiFeSe_Hases_2nde4ueqS1 A: beta meandersX: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)T: all-beta domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_2ndECOD (1.6)
I [auth S]NiFeSe_Hases_1ste4ueqS2 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: NiFeSe_Hases_1stECOD (1.6)
I [auth S]NiFeSe_Hases_3rde4ueqS4 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rdECOD (1.6)
I [auth S]NiFeSe_Hases_3rd_1e4ueqS3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)
J [auth T]NiFeSe_Hases_2nde4ueqT4 A: beta meandersX: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)T: all-beta domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_2ndECOD (1.6)
J [auth T]NiFeSe_Hases_1ste4ueqT2 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: NiFeSe_Hases_1stECOD (1.6)
J [auth T]NiFeSe_Hases_3rde4ueqT1 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rdECOD (1.6)
J [auth T]NiFeSe_Hases_3rd_1e4ueqT3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)
K [auth U]NiFeSe_Hases_2nde4ueqU3 A: beta meandersX: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)T: all-beta domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_2ndECOD (1.6)
K [auth U]NiFeSe_Hases_1ste4ueqU1 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: NiFeSe_Hases_1stECOD (1.6)
K [auth U]NiFeSe_Hases_3rde4ueqU2 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rdECOD (1.6)
K [auth U]NiFeSe_Hases_3rd_1e4ueqU4 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)
L [auth V]NiFeSe_Hases_2nde4ueqV2 A: beta meandersX: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)H: all-beta domain in nickel-iron hydrogenase large subunit (From Topology)T: all-beta domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_2ndECOD (1.6)
L [auth V]NiFeSe_Hases_1ste4ueqV4 A: alpha complex topologyX: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)H: alpha-helical domain in nickel-iron hydrogenase, large subunit (From Topology)T: alpha-helical domain in nickel-iron hydrogenase, large subunitF: NiFeSe_Hases_1stECOD (1.6)
L [auth V]NiFeSe_Hases_3rde4ueqV1 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rdECOD (1.6)
L [auth V]NiFeSe_Hases_3rd_1e4ueqV3 A: a+b two layersX: FAD-linked reductases, C-terminal domain-likeH: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology)T: Ni-Fe binding domain in nickel-iron hydrogenase large subunitF: NiFeSe_Hases_3rd_1ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
A3.40.50.700 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NADH:ubiquinone oxidoreductase-like, 20kDa subunitCATH (4.3.0)
A4.10.480.10 Few Secondary Structures Irregular Cytochrome-c3 Hydrogenase Chain A, domain 2CATH (4.3.0)
B3.40.50.700 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NADH:ubiquinone oxidoreductase-like, 20kDa subunitCATH (4.3.0)
B4.10.480.10 Few Secondary Structures Irregular Cytochrome-c3 Hydrogenase Chain A, domain 2CATH (4.3.0)
C3.40.50.700 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NADH:ubiquinone oxidoreductase-like, 20kDa subunitCATH (4.3.0)
C4.10.480.10 Few Secondary Structures Irregular Cytochrome-c3 Hydrogenase Chain A, domain 2CATH (4.3.0)
D3.40.50.700 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NADH:ubiquinone oxidoreductase-like, 20kDa subunitCATH (4.3.0)
D4.10.480.10 Few Secondary Structures Irregular Cytochrome-c3 Hydrogenase Chain A, domain 2CATH (4.3.0)
E3.40.50.700 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NADH:ubiquinone oxidoreductase-like, 20kDa subunitCATH (4.3.0)
E4.10.480.10 Few Secondary Structures Irregular Cytochrome-c3 Hydrogenase Chain A, domain 2CATH (4.3.0)
F3.40.50.700 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold NADH:ubiquinone oxidoreductase-like, 20kDa subunitCATH (4.3.0)
F4.10.480.10 Few Secondary Structures Irregular Cytochrome-c3 Hydrogenase Chain A, domain 2CATH (4.3.0)
G [auth Q]1.10.645.10 Mainly Alpha Orthogonal Bundle Cytochrome-c3 Hydrogenase chain BCATH (4.3.0)
H [auth R]1.10.645.10 Mainly Alpha Orthogonal Bundle Cytochrome-c3 Hydrogenase chain BCATH (4.3.0)
I [auth S]1.10.645.10 Mainly Alpha Orthogonal Bundle Cytochrome-c3 Hydrogenase chain BCATH (4.3.0)
J [auth T]1.10.645.10 Mainly Alpha Orthogonal Bundle Cytochrome-c3 Hydrogenase chain BCATH (4.3.0)
K [auth U]1.10.645.10 Mainly Alpha Orthogonal Bundle Cytochrome-c3 Hydrogenase chain BCATH (4.3.0)
L [auth V]1.10.645.10 Mainly Alpha Orthogonal Bundle Cytochrome-c3 Hydrogenase chain BCATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF14720NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C)NiFe/NiFeSe hydrogenase small subunit C-terminal- Family
A, B, C, D, E
PF01058NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)NADH ubiquinone oxidoreductase, 20 Kd subunitDomain
PF00374Nickel-dependent hydrogenase (NiFeSe_Hases)Nickel-dependent hydrogenase- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D, E
HYDROGENASE (NIFE) SMALL SUBUNIT HYDA
NICKEL-DEPENDENT HYDROGENASE LARGE SUBUNIT -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR006311Twin-arginine translocation pathway, signal sequenceConserved Site
A, B, C, D, E
IPR001821[NiFe]-hydrogenase, small subunitFamily
A, B, C, D, E
IPR027394Cytochrome-c3 hydrogenase, C-terminalDomain
A, B, C, D, E
IPR006137NADH:ubiquinone oxidoreductase-like, 20kDa subunitDomain
A, B, C, D, E
IPR037024[NiFe]-hydrogenase, small subunit, N-terminal domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR019546Twin-arginine translocation pathway, signal sequence, bacterial/archaealConserved Site
A, B, C, D, E
IPR037148[NiFe]-hydrogenase, small subunit, C-terminal domain superfamilyHomologous Superfamily
IPR001501Nickel-dependent hydrogenase, large subunitFamily
IPR029014[NiFe]-hydrogenase, large subunitHomologous Superfamily
IPR018194Nickel-dependent hydrogenase, large subunit, nickel binding siteBinding Site
IPR050867[NiFe]/[NiFeSe] hydrogenase large subunitFamily

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
CSS Parent Component: CYS

RESIDAA0269

PSI-MOD :  L-cysteine persulfide MOD:00274