3C8Y

1.39 Angstrom crystal structure of Fe-only hydrogenase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3c8ya1	Alpha and beta proteins (a/b)	Fe-only hydrogenase	Fe-only hydrogenase	Fe-only hydrogenase	Fe-only hydrogenase, catalytic domain	(Clostridium pasteurianum ) [TaxId: 1501 ],	SCOPe (2.08)
A	d3c8ya2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	2Fe-2S ferredoxin-like	2Fe-2S ferredoxin domains from multidomain proteins	Fe-only hydrogenase, N-terminal domain	(Clostridium pasteurianum ) [TaxId: 1501 ],	SCOPe (2.08)
A	d3c8ya3	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Fe-only hydrogenase, second domain	(Clostridium pasteurianum ) [TaxId: 1501 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Fe-only hydrogenase	8027408	4000867	SCOP2 (2022-06-29)
A	SCOP2 Family	2Fe-2S ferredoxin domains from multidomain proteins	8027410	4000241	SCOP2 (2022-06-29)
A	SCOP2 Family	Ferredoxin domains from multidomain proteins	8027413	4000021	SCOP2 (2022-06-29)
A	SCOP2 Family	Fe-only hydrogenase smaller subunit	8101148	4001528	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Fe-only hydrogenase	8039787	3001826	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	2Fe-2S ferredoxin-like	8039789	3000113	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	4Fe-4S ferredoxins	8039792	3000020	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Fe-only hydrogenase smaller subunit	8101149	3001779	SCOP2 (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_7_1	e3c8yA3	A: a+b two layers	X: 4Fe-4S ferredoxin (From Topology)	H: 4Fe-4S ferredoxin (From Topology)	T: 4Fe-4S ferredoxin	F: Fer4_7_1	ECOD (1.6)
A	Fer2_4	e3c8yA4	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Fer2_4	ECOD (1.6)
A	Fe_hyd_lg_C	e3c8yA5	A: a/b three-layered sandwiches	X: Fe-only hydrogenase (From Topology)	H: Fe-only hydrogenase (From Topology)	T: Fe-only hydrogenase	F: Fe_hyd_lg_C	ECOD (1.6)
A	NuoG_1st	e3c8yA2	A: extended segments	X: iron-sulfur center-binding helical hairpin (From Topology)	H: iron-sulfur center-binding helical hairpin (From Topology)	T: iron-sulfur center-binding helical hairpin	F: NuoG_1st	ECOD (1.6)
A	Fe_hyd_SSU	e3c8yA1	A: extended segments	X: Fe-only hydrogenase smaller subunit (From Topology)	H: Fe-only hydrogenase smaller subunit (From Topology)	T: Fe-only hydrogenase smaller subunit	F: Fe_hyd_SSU	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.20.740	Alpha Beta	Roll	Ubiquitin-like (UB roll)		CATH (4.3.0)
A	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF22609	Iron hydrogenase 1-like, iron-sulfur centre-binding domain (Fe_hydrogense_Fe-S_bd)	Iron hydrogenase 1-like, iron-sulfur centre-binding domain	This entry represents a Fe-S centre binding domain found in iron hydrogenases [1-5].	Domain
A	PF02906	Iron only hydrogenase large subunit, C-terminal domain (Fe_hyd_lg_C)	Iron only hydrogenase large subunit, C-terminal domain	-	Domain
A	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
A	PF02256	Iron hydrogenase small subunit (Fe_hyd_SSU)	Iron hydrogenase small subunit	This family represents the small subunit of the Fe-only hydrogenases EC:1.18.99.1. The subunit is comprised of alternating random coil and alpha helical structures that encompasses the large subunit in a novel protein fold [1].	Domain
A	PF13510	2Fe-2S iron-sulfur cluster binding domain (Fer2_4)	2Fe-2S iron-sulfur cluster binding domain	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. Th ...	The 2Fe-2S ferredoxin family have a general core structure consisting of beta(2)-alpha-beta(2) which a beta-grasp type fold. The domain is around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This cluster appears within sarcosine oxidase proteins.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Iron hydrogenase 1	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 cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster 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 cation binding transition metal ion binding iron ion binding ion binding binding metal ion binding small molecule binding iron-sulfur cluster binding 4 iron, 4 sulfur cluster binding metal cluster binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036010	2Fe-2S ferredoxin-like superfamily	Homologous Superfamily
A	IPR001041	2Fe-2S ferredoxin-type iron-sulfur binding domain	Domain
A	IPR009016	Iron hydrogenase	Homologous Superfamily
A	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
A	IPR004108	Iron hydrogenase, large subunit, C-terminal	Domain
A	IPR036991	Iron hydrogenase, small subunit superfamily	Homologous Superfamily
A	IPR050340	Cytosolic Fe-S Cluster Assembly Factor	Family
A	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
A	IPR013352	Iron hydrogenase, subset	Domain
A	IPR003149	Iron hydrogenase, small subunit	Domain
A	IPR019574	NADH:ubiquinone oxidoreductase, subunit G, iron-sulphur binding	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.