6YKB | pdb_00006ykb

[Fe]-hydrogenase from Methanolacinia paynteri in complex with GMP at 1.55-A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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	d6ykba2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Methanolacinia paynteri G-2000 ) [TaxId: 694436 ],	SCOPe (2.08)
A	d6ykba1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Methanolacinia paynteri G-2000 ) [TaxId: 694436 ],	SCOPe (2.08)
B [auth C]	d6ykbc2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	automated matches	automated matches	(Methanolacinia paynteri G-2000 ) [TaxId: 694436 ],	SCOPe (2.08)
B [auth C]	d6ykbc1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	automated matches	automated matches	(Methanolacinia paynteri G-2000 ) [TaxId: 694436 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	HMD	e6ykbA1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: HMD	ECOD (1.6)
A	PRK00961	e6ykbA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PRK00961	ECOD (1.6)
B [auth C]	HMD	e6ykbC1	A: alpha arrays	X: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	H: 6-phosphogluconate dehydrogenase C-terminal domain-like (From Topology)	T: 6-phosphogluconate dehydrogenase C-terminal domain-like	F: HMD	ECOD (1.6)
B [auth C]	PRK00961	e6ykbC2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PRK00961	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C]	PF03201	H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase (HMD)	H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase	-	Family
A, B [auth C]	PF22616	HMD N-terminal domain (HMD_N)	HMD N-terminal domain	This entry represents the N-terminal domain of 5,10-methenyltetrahydromethanopterin hydrogenase (HMD) and related proteins, an enzyme of the methanogenic energy metabolism [1-5]. HMD is an iron-sulphur-cluster-free enzyme that contains an intrinsic C ...	This entry represents the N-terminal domain of 5,10-methenyltetrahydromethanopterin hydrogenase (HMD) and related proteins, an enzyme of the methanogenic energy metabolism [1-5]. HMD is an iron-sulphur-cluster-free enzyme that contains an intrinsic CO ligand bound to iron. This domain has a Rossmann fold-like structure that contains a mononucleotide-binding site, which could harbour the GMP moiety of the cofactor [1-5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C]	5,10-methenyltetrahydromethanopterin [Fe]-hydrogenase	oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity oxidoreductase activity, acting on hydrogen as donor N5,N10-methenyltetrahydromethanopterin hydrogenase 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 methanogenesis, from carbon dioxide 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 methanogenesis, from carbon dioxide anaerobic respiration small molecule metabolic process one-carbon metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C]	IPR038182	HMD, C-terminal domain superfamily	Homologous Superfamily
A, B [auth C]	IPR024190	Methenyltetrahydromethanopterin dehydrogenase, Hmd-type	Family
A, B [auth C]	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B [auth C]	IPR004889	H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal	Domain
A, B [auth C]	IPR055205	5,10-methenyltetrahydromethanopterin hydrogenase, N-terminal domain	Domain
A, B [auth C]	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A, B [auth C]	IPR010062	5,10-methenyltetrahydromethanopterin hydrogenase	Family

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.