7UTD | pdb_00007utd

The 2.19-angstrom CryoEM structure of the [NiFe]-hydrogenase Huc from Mycobacterium smegmatis - Complex minus stalk

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	PH	e7utdA1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PH	ECOD (develop294)
C	PH	e7utdC1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PH	ECOD (develop294)
E	PH	e7utdE1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PH	ECOD (develop294)
G	PH	e7utdG1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PH	ECOD (develop294)
I	PH	e7utdI1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PH	ECOD (develop294)
K	PH	e7utdK1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PH	ECOD (develop294)
M	PH	e7utdM1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PH	ECOD (develop294)
O	PH	e7utdO1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: PH	ECOD (develop294)
B	RNA_pol_Rpb1_5	e7utdB01	A: alpha bundles	X: Rossmann-like	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: RNA_pol_Rpb1_5	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G, I A, C, E, G, I, K, M, O	PF00374	Nickel-dependent hydrogenase (NiFeSe_Hases)	Nickel-dependent hydrogenase	-	Family
B, D, F, H, J B, D, F, H, J, L, N, P	PF14720	NiFe/NiFeSe hydrogenase small subunit C-terminal (NiFe_hyd_SSU_C)	NiFe/NiFeSe hydrogenase small subunit C-terminal	-	Family
B, D, F, H, J B, D, F, H, J, L, N, P	PF01058	NADH ubiquinone oxidoreductase, 20 Kd subunit (Oxidored_q6)	NADH ubiquinone oxidoreductase, 20 Kd subunit		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G, I A, C, E, G, I, K, M, O	Hydrogenase-2, large subunit	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	-	cellular anatomical structure cell envelope
B, D, F, H, J B, D, F, H, J, L, N, P	Hydrogenase-2, small subunit	oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding hydrogenase (acceptor) activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor, iron-sulfur protein as acceptor oxidoreductase activity, acting on hydrogen as donor ferredoxin hydrogenase activity catalytic activity iron-sulfur cluster binding binding 3 iron, 4 sulfur cluster binding metal cluster binding small molecule binding hydrogenase (acceptor) activity 4 iron, 4 sulfur cluster binding electron transfer activity cation binding ion binding metal ion binding	cellular respiration energy derivation by oxidation of organic compounds metabolic process cellular process generation of precursor metabolites and energy anaerobic respiration	cellular anatomical structure membrane protein-containing complex catalytic complex oxidoreductase complex ferredoxin hydrogenase complex intracellular protein-containing complex [Ni-Fe] hydrogenase complex cell envelope
Q, R, S, T	Type 2 [NiFe]-hydrogenase Huc membrane adapter subunit	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G, I A, C, E, G, I, K, M, O	IPR001501	Nickel-dependent hydrogenase, large subunit	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR029014	[NiFe]-hydrogenase, large subunit	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR018194	Nickel-dependent hydrogenase, large subunit, nickel binding site	Binding Site
A, C, E, G, I A, C, E, G, I, K, M, O	IPR050867	[NiFe]/[NiFeSe] hydrogenase large subunit	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR001821	[NiFe]-hydrogenase, small subunit	Family
B, D, F, H, J B, D, F, H, J, L, N, P	IPR027394	Cytochrome-c3 hydrogenase, C-terminal	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR006137	NADH:ubiquinone oxidoreductase-like, 20kDa subunit	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR037024	[NiFe]-hydrogenase, small subunit, N-terminal domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR037148	[NiFe]-hydrogenase, small subunit, C-terminal domain superfamily	Homologous Superfamily
Q, R, S, T	IPR012440	Helical membrane plugin domain	Domain

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.