5ODI

Heterodisulfide reductase / [NiFe]-hydrogenase complex from Methanothermococcus thermolithotrophicus cocrystallized with CoM-SH

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d5odif_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Methanothermococcus thermolithotrophicus DSM 2095 ) [TaxId: 523845 ],	SCOPe (2.08)
L	d5odil_	Multi-domain proteins (alpha and beta)	HydB/Nqo4-like	HydB/Nqo4-like	automated matches	automated matches	(Methanothermococcus thermolithotrophicus DSM 2095 ) [TaxId: 523845 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2 Family	Nickel-iron hydrogenase, large subunit	8096641	4002888	SCOP2 (2022-06-29)
F	SCOP2 Superfamily	HydB/Nqo4-like	8096642	3001849	SCOP2 (2022-06-29)
L	SCOP2B Superfamily	HydB/Nqo4-like	8096642	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	Fer4_21_1	e5odiA3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
A	FAD_binding_3_1st	e5odiA1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: FAD_binding_3_1st	ECOD (1.6)
A	Pyr_redox_2	e5odiA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
G	Fer4_21_1	e5odiG3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_21_1	ECOD (1.6)
G	FAD_binding_3_1st	e5odiG1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: FAD_binding_3_1st	ECOD (1.6)
G	Pyr_redox_2	e5odiG2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Pyr_redox_2	ECOD (1.6)
B	CoB_CoM_SS_B_like	e5odiB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: CoB_CoM_SS_B_like	ECOD (1.6)
B	UNK_F_TYPE	e5odiB2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: UNK_F_TYPE	ECOD (1.6)
H	CoB_CoM_SS_B_like	e5odiH2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: CoB_CoM_SS_B_like	ECOD (1.6)
H	UNK_F_TYPE	e5odiH1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: ATC-like	F: UNK_F_TYPE	ECOD (1.6)
C	Fer4_8	e5odiC1	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
I	Fer4_8	e5odiI1	A: alpha arrays	X: alpha-helical ferredoxin-like	H: alpha-helical ferredoxin (From Topology)	T: alpha-helical ferredoxin	F: Fer4_8	ECOD (1.6)
D	UNK_F_TYPE	e5odiD1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Methyl-viologen reducing hydrogenase subunit D (From Topology)	T: Methyl-viologen reducing hydrogenase subunit D	F: UNK_F_TYPE	ECOD (1.6)
J	UNK_F_TYPE	e5odiJ1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Methyl-viologen reducing hydrogenase subunit D (From Topology)	T: Methyl-viologen reducing hydrogenase subunit D	F: UNK_F_TYPE	ECOD (1.6)
E	Oxidored_q6	e5odiE1	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	UNK_F_TYPE	e5odiE2	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: UNK_F_TYPE	ECOD (1.6)
K	Oxidored_q6	e5odiK1	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	UNK_F_TYPE	e5odiK2	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: UNK_F_TYPE	ECOD (1.6)
F	NiFeSe_Hases_1st	e5odiF4	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	NiFeSe_Hases_3rd	e5odiF1	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	NiFeSe_Hases_3rd_1	e5odiF3	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	NiFeSe_Hases_1st	e5odiL4	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	NiFeSe_Hases_3rd	e5odiL2	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	NiFeSe_Hases_3rd_1	e5odiL3	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, G	PF13187	4Fe-4S dicluster domain (Fer4_9)	4Fe-4S dicluster domain	-	Family
A, G	PF00890	FAD binding domain (FAD_binding_2)	FAD binding domain	-	Family
A, G	PF12838	4Fe-4S dicluster domain (Fer4_7)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
B, H	PF02754	Cysteine-rich domain (CCG)	Cysteine-rich domain	-	Family
C, I	PF13183	4Fe-4S dicluster domain (Fer4_8)	4Fe-4S dicluster domain	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contai ...	Superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases. Structure of the domain is an alpha-antiparallel beta sandwich. Domain contains two 4Fe4S clusters.	Domain
D, J	PF02662	Methyl-viologen-reducing hydrogenase, delta subunit (FlpD)	Methyl-viologen-reducing hydrogenase, delta subunit	-	Family
E, K	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit	-	Family
F, L	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, G	Heterodisulfide reductase, subunit A	oxidoreductase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding nucleoside phosphate binding organic cyclic compound binding nucleotide binding heterocyclic compound binding cation binding ion binding metal ion binding	-	-
B, H	Heterodisulfide reductase, subunit B	oxidoreductase activity, acting on a sulfur group of donors CoB--CoM heterodisulfide reductase activity oxidoreductase activity catalytic activity	cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process alkane metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
C, I	Heterodisulfide reductase, subunit C	oxidoreductase activity, acting on a sulfur group of donors CoB--CoM heterodisulfide reductase activity oxidoreductase activity catalytic activity iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon metabolic process alkane metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
D, J	Methyl-viologen reducing hydrogenase, subunit D	oxidoreductase activity, acting on a sulfur group of donors CoB--CoM heterodisulfide reductase activity oxidoreductase activity catalytic activity iron-sulfur cluster binding 2 iron, 2 sulfur cluster binding binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-
E, K	Methyl-viologen reducing hydrogenase, subunit G	hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity hydrogen dehydrogenase activity oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor iron-sulfur cluster binding binding 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding ion binding metal ion binding	-	-
F, L	Methyl-viologen reducing hydrogenase, subunit A	hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity hydrogen dehydrogenase activity hydrogenase (acceptor) activity oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor catalytic activity cation binding transition metal ion binding ion binding binding nickel cation binding metal ion binding small molecule binding oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor ferredoxin hydrogenase activity hydrogen dehydrogenase activity oxidoreductase activity, acting on hydrogen as donor, NAD or NADP as acceptor	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, G	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, G	IPR039650	H(2):CoB-CoM heterodisulfide,ferredoxin reductase subunit A-like	Family
A, G	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A, G	IPR036188	FAD/NAD(P)-binding domain superfamily	Homologous Superfamily
A, G	IPR003953	FAD-dependent oxidoreductase 2, FAD binding domain	Domain
B, H	IPR004017	Cysteine-rich domain	Domain
B, H	IPR017678	CoB--CoM heterodisulphide reductase, subunit B	Family
B, H	IPR051278	CoM-S-S-CoB heterodisulfide reductase	Family
C, I	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
C, I	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
C, I	IPR051460	Heterodisulfide reductase iron-sulfur subunit C	Family
C, I	IPR017680	CoB--CoM heterodisulphide reductase, subunit C	Family
C, I	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
D, J	IPR003813	F420-non-reducing hydrogenase iron-sulfur subunit D	Domain
E, K	IPR051349	Hydrogenase complex-associated protein	Family
E, K	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
E, K	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
F, L	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
F, L	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
F, L	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
B	ferredoxin:CoB-CoM heterodisulfide reductase M-CSA #981	Methyl-coenzyme M (methyl-S-CoM) and coenzyme B (HS-CoB) form the heterodisulfide CoM-S-S-CoB which can be reduced back to HS-CoB and HS-CoM by the HdrABC enzyme complex. The reaction takes place in the HdrB subunit of the HdrABC-MvhAGD complex, which is of interest because it catalyses an iron-sulfur cluster-assisted disulfide reduction mechanism. HdrB adopts an aspartate racemase-like fold with two similar noncubane [4Fe-4S] clusters composed of highly distorted [3Fe-3S] and [2Fe-2S] subclusters. The subunit contains a duplicated CCG motif which is predicted to be a binding motif for iron-sulfur clusters.	Defined by 11 residues: CYS:B-9CYS:B-41CYS:B-42CYS:B-78CYS:B-81CYS:B-153HIS:B-154CYS:B-193CYS:B-194CYS:B-231CYS:B-234 \| Explore in 3D: M-CSA Motif Definition Up to 10 residues are supported for Structure Motif searching, this motif has 11 residues. EC: 1.8.98.1 (PDB Primary Data)