1LU9 | pdb_00001lu9

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1

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)
C	d1lu9c1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Aminoacid dehydrogenase-like, C-terminal domain	Methylene-tetrahydromethanopterin dehydrogenase	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
C	d1lu9c2	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Methylene-tetrahydromethanopterin dehydrogenase	Methylene-tetrahydromethanopterin dehydrogenase	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
B	d1lu9b1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Aminoacid dehydrogenase-like, C-terminal domain	Methylene-tetrahydromethanopterin dehydrogenase	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
B	d1lu9b2	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Methylene-tetrahydromethanopterin dehydrogenase	Methylene-tetrahydromethanopterin dehydrogenase	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
A	d1lu9a1	Alpha and beta proteins (a/b)	NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	Aminoacid dehydrogenase-like, C-terminal domain	Methylene-tetrahydromethanopterin dehydrogenase	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)
A	d1lu9a2	Alpha and beta proteins (a/b)	Aminoacid dehydrogenase-like, N-terminal domain	Aminoacid dehydrogenase-like, N-terminal domain	Methylene-tetrahydromethanopterin dehydrogenase	Methylene-tetrahydromethanopterin dehydrogenase	(Methylorubrum extorquens AM1 ) [TaxId: 272630 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	MtdA-like	8001046	3000046	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	MtdA-like	8001046	3000046	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	MtdA-like	8001046	3000046	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)
C	NAD_binding_10	e1lu9C1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_10	ECOD (1.6)
C	Mpt_N	e1lu9C2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: Mpt_N	ECOD (1.6)
B	NAD_binding_10	e1lu9B1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_10	ECOD (1.6)
B	Mpt_N	e1lu9B2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: Mpt_N	ECOD (1.6)
A	NAD_binding_10	e1lu9A1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: NAD(P)-binding Rossmann-fold domains	F: NAD_binding_10	ECOD (1.6)
A	Mpt_N	e1lu9A2	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Class I glutamine amidotransferase-like	T: Aminoacid dehydrogenase-like, N-terminal domain	F: Mpt_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	3.40.50.10280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain	CATH (4.3.0)
C	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
B	3.40.50.10280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain	CATH (4.3.0)
B	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)
A	3.40.50.10280	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain	CATH (4.3.0)
A	3.40.50.720	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	NAD(P)-binding Rossmann-like Domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF09176	Methylene-tetrahydromethanopterin dehydrogenase, N-terminal (Mpt_N)	Methylene-tetrahydromethanopterin dehydrogenase, N-terminal	Members of this family adopt a alpha-beta structure, with a core comprising three alpha/beta/alpha layers, in which each sheet contains four strands. They are predominantly found in prokaryotic methylene-tetrahydromethanopterin dehydrogenase, which c ...	Members of this family adopt a alpha-beta structure, with a core comprising three alpha/beta/alpha layers, in which each sheet contains four strands. They are predominantly found in prokaryotic methylene-tetrahydromethanopterin dehydrogenase, which catalyses the dehydrogenation of methylene-tetrahydromethanopterin and the reversible dehydrogenation of methylene-H(4)F [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Methylene Tetrahydromethanopterin Dehydrogenase	methylenetetrahydrofolate dehydrogenase (NADP+) activity 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 catalytic activity	cellular response to stimulus cellular detoxification catabolic process response to stimulus formaldehyde catabolic process detoxification response to oxygen-containing compound cellular response to oxygen-containing compound aldehyde metabolic process response to toxic substance cellular detoxification of aldehyde cellular response to chemical stimulus cellular response to aldehyde response to chemical cellular response to stimulus cellular detoxification catabolic process response to stimulus formaldehyde catabolic process detoxification response to oxygen-containing compound cellular response to oxygen-containing compound aldehyde metabolic process response to toxic substance cellular detoxification of aldehyde cellular response to chemical stimulus cellular response to aldehyde response to chemical metabolic process cellular process small molecule metabolic process formaldehyde metabolic process aldehyde catabolic process small molecule catabolic process cellular response to toxic substance one-carbon metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR037089	Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR036291	NAD(P)-binding domain superfamily	Homologous Superfamily
A, B, C	IPR046346	Aminoacid dehydrogenase-like, N-terminal domain superfamily	Homologous Superfamily
A, B, C	IPR035015	Methylene tetrahydromethanopterin dehydrogenase, NADP-binding domain	Domain
A, B, C	IPR015259	Methylene-tetrahydromethanopterin dehydrogenase, N-terminal	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.