1Z69 | pdb_00001z69

Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420

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)
D	d1z69d_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Bacterial luciferase-like	automated matches	automated matches	(Methanosarcina barkeri ) [TaxId: 2208 ],	SCOPe (2.08)
C	d1z69c_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Bacterial luciferase-like	automated matches	automated matches	(Methanosarcina barkeri ) [TaxId: 2208 ],	SCOPe (2.08)
B	d1z69b_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Bacterial luciferase-like	automated matches	automated matches	(Methanosarcina barkeri ) [TaxId: 2208 ],	SCOPe (2.08)
A	d1z69a_	Alpha and beta proteins (a/b)	TIM beta/alpha-barrel	Bacterial luciferase-like	automated matches	automated matches	(Methanosarcina barkeri ) [TaxId: 2208 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Bacterial luciferase-like	8085536	3000585	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bacterial luciferase-like	8085536	3000585	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacterial luciferase-like	8085536	3000585	SCOP2B (2022-06-29)
A	SCOP2 Family	F420 dependent oxidoreductases	8085535	4003322	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Bacterial luciferase-like	8085536	3000585	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)
D	Bac_luciferase	e1z69D1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Bac_luciferase	ECOD (1.6)
C	Bac_luciferase	e1z69C1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Bac_luciferase	ECOD (1.6)
B	Bac_luciferase	e1z69B1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Bac_luciferase	ECOD (1.6)
A	Bac_luciferase	e1z69A1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: Bac_luciferase	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.20.20.30	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Luciferase-like domain	CATH (4.2.0)
C	3.20.20.30	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Luciferase-like domain	CATH (4.2.0)
B	3.20.20.30	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Luciferase-like domain	CATH (4.2.0)
A	3.20.20.30	Alpha Beta	Alpha-Beta Barrel	TIM Barrel	Luciferase-like domain	CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00296	Luciferase-like monooxygenase (Bac_luciferase)	Luciferase-like monooxygenase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Coenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase	oxidoreductase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen catalytic activity coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity oxidoreductase activity, acting on the CH-NH group of donors	cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon 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 cellular respiration energy derivation by oxidation of organic compounds alkane biosynthetic process methane metabolic process generation of precursor metabolites and energy hydrocarbon 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	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050564	F420-dependent glucose-6-phosphate dehydrogenase/mer	Family
A, B, C, D	IPR011251	Luciferase-like domain	Domain
A, B, C, D	IPR019946	5,10-methylenetetrahydromethanopterin reductase	Family
A, B, C, D	IPR036661	Luciferase-like domain superfamily	Homologous Superfamily

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.