5ODI | pdb_00005odi

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
Domain Annotation: CATH
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)
F	Histone	e5odiF4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Histone	ECOD (v294.1)
F	L_protein_N	e5odiF1	A: a/b three-layered sandwiches	X: Family A G protein-coupled receptor-like	H: beta-sandwich domain in metalloprotease stcE	T: Restriction endonuclease-like	F: L_protein_N	ECOD (v294.1)
L	Complex1_30kDa	e5odiL2	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Complex1_30kDa	ECOD (v294.1)
L	BNR_6, Sortilin-Vps10	e5odiL4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: Hemagglutinin HA2 chain	T: Hemagglutinin HA2 chain	F: BNR_6, Sortilin-Vps10	ECOD (v294.1)
E	FATC	e5odiE1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: FATC	ECOD (v294.1)
K	FATC	e5odiK1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: FATC	ECOD (v294.1)
D	BPA_C	e5odiD1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: BPA_C	ECOD (v294.1)
J	BPA_C	e5odiJ1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: BPA_C	ECOD (v294.1)
C	BPA_C	e5odiC1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: BPA_C	ECOD (v294.1)
I	BPA_C	e5odiI1	A: a/b three-layered sandwiches	X: Phosphorylase/hydrolase-like	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: BPA_C	ECOD (v294.1)
B	FATC	e5odiB1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: FATC	ECOD (v294.1)
H	FATC	e5odiH1	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: FATC	ECOD (v294.1)
A	Histone	e5odiA1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Histone	ECOD (v294.1)
G	Histone	e5odiG1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Histone	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
E	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (utative)
K	3.40.50.700	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	CATH (utative)
B	1.20.1050.140	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (utative)
H	1.20.1050.140	Mainly Alpha	Up-down Bundle	Glutathione S-transferase Yfyf (Class Pi)	Chain A, domain 2	CATH (utative)
A	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)
G	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	-	-
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	-	-
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	-	-
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 biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	cell periphery cellular anatomical structure plasma membrane membrane
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 biosynthetic process energy derivation by oxidation of reduced inorganic compounds methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
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 nucleotide binding heterocyclic compound binding cation binding ion binding metal ion binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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
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
D, J	IPR003813	F420-non-reducing hydrogenase iron-sulfur subunit D	Domain
C, I	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
C, I	IPR051460	HdrC_iron-sulfur_subunit	Unknown
C, I	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
C, I	IPR017680	CoB--CoM heterodisulphide reductase, subunit C	Family
C, I	IPR009051	Alpha-helical ferredoxin	Homologous Superfamily
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
A, G	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A, G	IPR003953	FAD-dependent oxidoreductase 2, FAD-binding domain	Domain
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

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)

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

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