3DAG

The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII

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	d3daga2	All alpha proteins	6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	HMD dimerization domain-like	5,10-methenyltetrahydromethanopterin hydrogenase, HMD	Methanococcus jannaschii (Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
A	d3daga1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase-like, N-terminal domain	5,10-methenyltetrahydromethanopterin hydrogenase, HMD	Methanococcus jannaschii (Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	6-phosphogluconate dehydrogenase-like	8001190	3000048	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)
A	HMD	e3dagA1	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	e3dagA2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: PRK00961	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	1.20.120.1300	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Hmd, C-terminal helical subdomain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03201	H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase (HMD)	H2-forming N5,N10-methylene-tetrahydromethanopterin dehydrogenase	-	Family
A	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	5,10-methenyltetrahydromethanopterin hydrogenase	oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors pyrroline-5-carboxylate reductase activity catalytic activity oxidoreductase activity, acting on hydrogen as donor, with other known acceptors oxidoreductase activity, acting on hydrogen as donor N5,N10-methenyltetrahydromethanopterin hydrogenase activity	glutamine family amino acid biosynthetic process oxoacid metabolic process amino acid metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process proline metabolic process small molecule metabolic process proline biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process glutamine family amino acid biosynthetic process oxoacid metabolic process amino acid metabolic process L-proline biosynthetic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glutamine family amino acid metabolic process proline metabolic process small molecule metabolic process proline biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process metabolic process cellular process alpha-amino acid biosynthetic process 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 energy derivation by oxidation of reduced inorganic compounds methanogenesis hydrocarbon biosynthetic process methanogenesis, from carbon dioxide anaerobic respiration one-carbon metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038182	HMD, C-terminal domain superfamily	Homologous Superfamily
A	IPR024190	Methenyltetrahydromethanopterin dehydrogenase, Hmd-type	Family
A	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A	IPR004889	H2-forming N5,N10-methylenetetrahydromethanopterin dehydrogenase, C-terminal	Domain
A	IPR008927	6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily	Homologous Superfamily
A	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.