1HFE

1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS

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
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)
B [auth L]	d1hfel1	Alpha and beta proteins (a/b)	Fe-only hydrogenase	Fe-only hydrogenase	Fe-only hydrogenase	Fe-only hydrogenase larger subunit, C-domain	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
B [auth L]	d1hfel2	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Fe-only hydrogenase larger subunit, N-domain	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
D [auth M]	d1hfem1	Alpha and beta proteins (a/b)	Fe-only hydrogenase	Fe-only hydrogenase	Fe-only hydrogenase	Fe-only hydrogenase larger subunit, C-domain	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
D [auth M]	d1hfem2	Alpha and beta proteins (a+b)	Ferredoxin-like	4Fe-4S ferredoxins	Ferredoxin domains from multidomain proteins	Fe-only hydrogenase larger subunit, N-domain	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
A [auth S]	d1hfes_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Fe-only hydrogenase smaller subunit	Fe-only hydrogenase smaller subunit	Fe-only hydrogenase smaller subunit	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)
C [auth T]	d1hfet_	All alpha proteins	Non-globular all-alpha subunits of globular proteins	Fe-only hydrogenase smaller subunit	Fe-only hydrogenase smaller subunit	Fe-only hydrogenase smaller subunit	(Nitratidesulfovibrio vulgaris str. Hildenborough ) [TaxId: 882 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth L]	SCOP2 Family	Fe-only hydrogenase	8021061	4000867	SCOP2 (2022-06-29)
B [auth L]	SCOP2 Family	Ferredoxin domains from multidomain proteins	8022773	4000021	SCOP2 (2022-06-29)
B [auth L]	SCOP2 Superfamily	Fe-only hydrogenase	8033441	3001826	SCOP2 (2022-06-29)
B [auth L]	SCOP2 Superfamily	4Fe-4S ferredoxins	8035153	3000020	SCOP2 (2022-06-29)
D [auth M]	SCOP2B Superfamily	4Fe-4S ferredoxins	8035153	3000020	SCOP2B (2022-06-29)
D [auth M]	SCOP2B Superfamily	Fe-only hydrogenase	8033441	3001826	SCOP2B (2022-06-29)
A [auth S]	SCOP2 Family	Fe-only hydrogenase smaller subunit	8026713	4001528	SCOP2 (2022-06-29)
A [auth S]	SCOP2 Superfamily	Fe-only hydrogenase smaller subunit	8039092	3001779	SCOP2 (2022-06-29)
C [auth T]	SCOP2B Superfamily	Fe-only hydrogenase smaller subunit	8039092	3001779	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)
B [auth L]	Fer4_21_1	e1hfeL2	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)
B [auth L]	Fe_hyd_lg_C	e1hfeL3	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)
D [auth M]	Fer4_21_1	e1hfeM2	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)
D [auth M]	Fe_hyd_lg_C	e1hfeM3	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 [auth S]	Fe_hyd_SSU	e1hfeS1	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)
C [auth T]	Fe_hyd_SSU	e1hfeT1	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)
B [auth L]	3.40.50.1780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
B [auth L]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B [auth L]	3.40.950.10	Alpha Beta	3-Layer(aba) Sandwich	Fe-only Hydrogenase (Larger Subunit)	Chain L, domain 3	CATH (4.3.0)
D [auth M]	3.40.50.1780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold		CATH (4.3.0)
D [auth M]	3.30.70.20	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D [auth M]	3.40.950.10	Alpha Beta	3-Layer(aba) Sandwich	Fe-only Hydrogenase (Larger Subunit)	Chain L, domain 3	CATH (4.3.0)
A [auth S]	4.10.260.20	Few Secondary Structures	Irregular	G Protein Gi Gamma 2	Iron hydrogenase, small subunit	CATH (4.3.0)
C [auth T]	4.10.260.20	Few Secondary Structures	Irregular	G Protein Gi Gamma 2	Iron hydrogenase, small subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth L], D [auth M]	PF02906	Iron only hydrogenase large subunit, C-terminal domain (Fe_hyd_lg_C)	Iron only hydrogenase large subunit, C-terminal domain		Domain
B [auth L], D [auth M]	PF00037	4Fe-4S binding domain (Fer4)	4Fe-4S binding 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
A [auth S], C [auth T]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth L], D [auth M]	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (LARGER 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 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion 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 4 iron, 4 sulfur cluster binding metal cluster binding small molecule binding cation binding transition metal ion binding iron ion binding ion binding metal ion binding	-	cellular anatomical structure periplasmic space
A [auth S], C [auth T]	PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) (SMALLER SUBUNIT))	iron-sulfur cluster binding binding metal cluster binding small molecule 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 electron transfer activity cation binding transition metal ion binding iron ion binding ion binding iron-sulfur cluster binding binding metal cluster binding small molecule 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 electron transfer activity cation binding transition metal ion binding iron ion binding ion binding metal ion binding	-	cellular anatomical structure periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth L], D [auth M]	IPR017900	4Fe-4S ferredoxin, iron-sulphur binding, conserved site	Conserved Site
B [auth L], D [auth M]	IPR004108	Iron hydrogenase, large subunit, C-terminal	Domain
B [auth L], D [auth M]	IPR050340	Cytosolic Fe-S Cluster Assembly Factor	Family
B [auth L], D [auth M]	IPR009016	Iron hydrogenase	Homologous Superfamily
B [auth L], D [auth M]	IPR017896	4Fe-4S ferredoxin-type, iron-sulphur binding domain	Domain
B [auth L], D [auth M]	IPR013352	Iron hydrogenase, subset	Domain
A [auth S], C [auth T]	IPR036991	Iron hydrogenase, small subunit superfamily	Homologous Superfamily
A [auth S], C [auth T]	IPR006311	Twin-arginine translocation pathway, signal sequence	Conserved Site
A [auth S], C [auth T]	IPR003149	Iron hydrogenase, small subunit	Domain
A [auth S], C [auth T]	IPR008953	Iron hydrogenase, small subunit HydB-type	Homologous Superfamily
A [auth S], C [auth T]	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal	Conserved Site

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

Chains	Enzyme Name	Description	Catalytic Residues
B [auth L]	ferredoxin hydrogenase M-CSA #127	The iron-only hydrogenase from Desulphovibrio desulphuricans is able to catalyse the heterolytic fission of molecular hydrogen to release protons and electrons. It is part of a family of iron-only hydrogenases which all have two iron centres at the active site, in contrast to the better known Ni-Fe hydrogenases with which they share no sequence or structural homology. The mechanism by which the hydrogenases work is of great interest to biologists and engineers alike as it offers the possibility of using hydrogen as a fuel more effectively.	Defined by 8 residues: GLU:B-156 [auth L-156]GLU:B-159 [auth L-159]CYS:B-178 [auth L-178]SER:B-198 [auth L-198]LYS:B-237 [auth L-237]GLU:B-240 [auth L-240]GLU:B-245 [auth L-245]CYS:B-382 [auth L-382] \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.18.99.1 (PDB Primary Data) Search M-CSA Motif + EC 1.18.99.1 EC: 1.12.7.2 (UniProt) Search M-CSA Motif + EC 1.12.7.2

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.