2FRV
CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE
External Resource: Annotation
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A [auth S] | SCOP2B Superfamily | HydA C-terminal domain-like | 8034854 | 3001861 | SCOP2B (2022-06-29) |
A [auth S] | SCOP2B Superfamily | Nqo6/HydA N-terminal domain-like | 8054417 | 3002291 | SCOP2B (2022-06-29) |
C [auth A] | SCOP2B Superfamily | HydA C-terminal domain-like | 8034854 | 3001861 | SCOP2B (2022-06-29) |
C [auth A] | SCOP2B Superfamily | Nqo6/HydA N-terminal domain-like | 8054417 | 3002291 | SCOP2B (2022-06-29) |
I [auth G] | SCOP2B Superfamily | Nqo6/HydA N-terminal domain-like | 8054417 | 3002291 | SCOP2B (2022-06-29) |
I [auth G] | SCOP2B Superfamily | HydA C-terminal domain-like | 8034854 | 3001861 | SCOP2B (2022-06-29) |
E [auth C] | SCOP2B Superfamily | HydA C-terminal domain-like | 8034854 | 3001861 | SCOP2B (2022-06-29) |
E [auth C] | SCOP2B Superfamily | Nqo6/HydA N-terminal domain-like | 8054417 | 3002291 | SCOP2B (2022-06-29) |
G [auth E] | SCOP2B Superfamily | Nqo6/HydA N-terminal domain-like | 8054417 | 3002291 | SCOP2B (2022-06-29) |
G [auth E] | SCOP2B Superfamily | HydA C-terminal domain-like | 8034854 | 3001861 | SCOP2B (2022-06-29) |
K [auth I] | SCOP2B Superfamily | HydA C-terminal domain-like | 8034854 | 3001861 | SCOP2B (2022-06-29) |
K [auth I] | SCOP2B Superfamily | Nqo6/HydA N-terminal domain-like | 8054417 | 3002291 | SCOP2B (2022-06-29) |
B [auth L] | SCOP2B Superfamily | HydB/Nqo4-like | 8032555 | 3001849 | SCOP2B (2022-06-29) |
D [auth B] | SCOP2B Superfamily | HydB/Nqo4-like | 8032555 | 3001849 | SCOP2B (2022-06-29) |
H [auth F] | SCOP2B Superfamily | HydB/Nqo4-like | 8032555 | 3001849 | SCOP2B (2022-06-29) |
J [auth H] | SCOP2B Superfamily | HydB/Nqo4-like | 8032555 | 3001849 | SCOP2B (2022-06-29) |
L [auth J] | SCOP2B Superfamily | HydB/Nqo4-like | 8032555 | 3001849 | SCOP2B (2022-06-29) |
F [auth D] | SCOP2B Superfamily | HydB/Nqo4-like | 8032555 | 3001849 | SCOP2B (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A [auth S] | Oxidored_q6 | e2frvS2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: Oxidored_q6 | ECOD (1.6) |
A [auth S] | NiFe_hyd_SSU_C | e2frvS1 | A: few secondary structure elements | X: 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 subunit | F: NiFe_hyd_SSU_C | ECOD (1.6) |
C [auth A] | Oxidored_q6 | e2frvA2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: Oxidored_q6 | ECOD (1.6) |
C [auth A] | NiFe_hyd_SSU_C | e2frvA1 | A: few secondary structure elements | X: 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 subunit | F: NiFe_hyd_SSU_C | ECOD (1.6) |
I [auth G] | Oxidored_q6 | e2frvG2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: Oxidored_q6 | ECOD (1.6) |
I [auth G] | NiFe_hyd_SSU_C | e2frvG1 | A: few secondary structure elements | X: 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 subunit | F: NiFe_hyd_SSU_C | ECOD (1.6) |
E [auth C] | Oxidored_q6 | e2frvC2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: Oxidored_q6 | ECOD (1.6) |
E [auth C] | NiFe_hyd_SSU_C | e2frvC1 | A: few secondary structure elements | X: 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 subunit | F: NiFe_hyd_SSU_C | ECOD (1.6) |
G [auth E] | Oxidored_q6 | e2frvE2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: Oxidored_q6 | ECOD (1.6) |
G [auth E] | NiFe_hyd_SSU_C | e2frvE1 | A: few secondary structure elements | X: 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 subunit | F: NiFe_hyd_SSU_C | ECOD (1.6) |
K [auth I] | Oxidored_q6 | e2frvI2 | A: a/b three-layered sandwiches | X: Flavodoxin-like | H: Class I glutamine amidotransferase-like | T: CheY-like | F: Oxidored_q6 | ECOD (1.6) |
K [auth I] | NiFe_hyd_SSU_C | e2frvI1 | A: few secondary structure elements | X: 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 subunit | F: NiFe_hyd_SSU_C | ECOD (1.6) |
B [auth L] | NiFeSe_Hases_2nd | e2frvL1 | A: beta meanders | X: 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 subunit | F: NiFeSe_Hases_2nd | ECOD (1.6) |
B [auth L] | NiFeSe_Hases_1st | e2frvL2 | A: alpha complex topology | X: 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 subunit | F: NiFeSe_Hases_1st | ECOD (1.6) |
B [auth L] | NiFeSe_Hases_3rd | e2frvL3 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd | ECOD (1.6) |
B [auth L] | NiFeSe_Hases_3rd_1 | e2frvL4 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd_1 | ECOD (1.6) |
D [auth B] | NiFeSe_Hases_2nd | e2frvB1 | A: beta meanders | X: 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 subunit | F: NiFeSe_Hases_2nd | ECOD (1.6) |
D [auth B] | NiFeSe_Hases_1st | e2frvB2 | A: alpha complex topology | X: 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 subunit | F: NiFeSe_Hases_1st | ECOD (1.6) |
D [auth B] | NiFeSe_Hases_3rd | e2frvB3 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd | ECOD (1.6) |
D [auth B] | NiFeSe_Hases_3rd_1 | e2frvB4 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd_1 | ECOD (1.6) |
H [auth F] | NiFeSe_Hases_2nd | e2frvF1 | A: beta meanders | X: 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 subunit | F: NiFeSe_Hases_2nd | ECOD (1.6) |
H [auth F] | NiFeSe_Hases_1st | e2frvF2 | A: alpha complex topology | X: 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 subunit | F: NiFeSe_Hases_1st | ECOD (1.6) |
H [auth F] | NiFeSe_Hases_3rd | e2frvF3 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd | ECOD (1.6) |
H [auth F] | NiFeSe_Hases_3rd_1 | e2frvF4 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd_1 | ECOD (1.6) |
J [auth H] | NiFeSe_Hases_2nd | e2frvH1 | A: beta meanders | X: 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 subunit | F: NiFeSe_Hases_2nd | ECOD (1.6) |
J [auth H] | NiFeSe_Hases_1st | e2frvH2 | A: alpha complex topology | X: 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 subunit | F: NiFeSe_Hases_1st | ECOD (1.6) |
J [auth H] | NiFeSe_Hases_3rd | e2frvH3 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd | ECOD (1.6) |
J [auth H] | NiFeSe_Hases_3rd_1 | e2frvH4 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd_1 | ECOD (1.6) |
L [auth J] | NiFeSe_Hases_2nd | e2frvJ1 | A: beta meanders | X: 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 subunit | F: NiFeSe_Hases_2nd | ECOD (1.6) |
L [auth J] | NiFeSe_Hases_1st | e2frvJ2 | A: alpha complex topology | X: 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 subunit | F: NiFeSe_Hases_1st | ECOD (1.6) |
L [auth J] | NiFeSe_Hases_3rd | e2frvJ3 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd | ECOD (1.6) |
L [auth J] | NiFeSe_Hases_3rd_1 | e2frvJ4 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd_1 | ECOD (1.6) |
F [auth D] | NiFeSe_Hases_2nd | e2frvD1 | A: beta meanders | X: 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 subunit | F: NiFeSe_Hases_2nd | ECOD (1.6) |
F [auth D] | NiFeSe_Hases_1st | e2frvD2 | A: alpha complex topology | X: 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 subunit | F: NiFeSe_Hases_1st | ECOD (1.6) |
F [auth D] | NiFeSe_Hases_3rd | e2frvD3 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd | ECOD (1.6) |
F [auth D] | NiFeSe_Hases_3rd_1 | e2frvD4 | A: a+b two layers | X: FAD-linked reductases, C-terminal domain-like | H: Ni-Fe binding domain in nickel-iron hydrogenase large subunit (From Topology) | T: Ni-Fe binding domain in nickel-iron hydrogenase large subunit | F: NiFeSe_Hases_3rd_1 | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF14720 | NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C) | NiFe/NiFeSe hydrogenase small subunit C-terminal | - | Family | |
PF01058 | NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6) | NADH ubiquinone oxidoreductase, 20 Kd subunit | - | Family | |
PF00374 | Nickel-dependent hydrogenase (NiFeSe_Hases) | Nickel-dependent hydrogenase | - | Family |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR001821 | [NiFe]-hydrogenase, small subunit | Family | |
IPR027394 | Cytochrome-c3 hydrogenase, C-terminal | Domain | |
IPR006137 | NADH:ubiquinone oxidoreductase-like, 20kDa subunit | Domain | |
IPR037024 | [NiFe]-hydrogenase, small subunit, N-terminal domain superfamily | Homologous Superfamily | |
IPR037148 | [NiFe]-hydrogenase, small subunit, C-terminal domain superfamily | Homologous Superfamily | |
IPR001501 | Nickel-dependent hydrogenase, large subunit | Family | |
IPR029014 | [NiFe]-hydrogenase, large subunit | Homologous Superfamily | |
IPR018194 | Nickel-dependent hydrogenase, large subunit, nickel binding site | Binding Site | |
IPR050867 | [NiFe]/[NiFeSe] hydrogenase large subunit | Family |
Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage
Chains | Enzyme Name | Description | Catalytic Residues |
---|---|---|---|
cytochrome-c3 hydrogenase M-CSA #126 | Hydrogenases are enzymes that catalyse the reversible heterolytic dissociation of molecular hydrogen H2 to two protons and two electrons. The largest class of hydrogenases contains a NiFe center that is believed to be the catalytic site for hydrogen activation.The active site comprises a heterobimetallic cluster of Ni and Fe atoms. The bridging ligand X is proposed to be sulphur species due to the release of H2S during the course of the reaction. Several alternative mechanisms exist for hydrogen activation by transition metal complexes. Generally these reactions proceed through either oxidative addition or sigma-bond metathesis (which is usually described as homolytic and without strong charge polarisation unless R is a polar group). Hydrogen isotope exchange and computational experiments for this enzyme indicate that the H-H cleavage reaction is heterolytic [PMID:11703120]. Cytochrome c3, the physiological electron acceptor for this particular hydrogenase, is a tetraheme cytochrome. The hemes all have different potentials, and probably only one or two are likely to accept electrons from the enzyme under physiological conditions. | Defined by 8 residues: GLU:F-18 [auth D-18]CYS:F-65 [auth D-65]CYS:F-68 [auth D-68]HIS:F-72 [auth D-72]ARG:F-463 [auth D-463]SER:F-486 [auth D-486]CYS:F-530 [auth D-530]CYS:F-533 [auth D-533] | EC: 1.18.99.1 (PDB Primary Data) EC: 1.12.2.1 (UniProt) |