3M2V

Structural Insight into Methyl-Coenzyme M Reductase Chemistry using Coenzyme B Analogues

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3m2va2	All alpha proteins	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Alpha chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
A	d3m2va1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase alpha and beta chain N-terminal domain	Alpha chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
D	d3m2vd2	All alpha proteins	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Alpha chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
D	d3m2vd1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase alpha and beta chain N-terminal domain	Alpha chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
B	d3m2vb2	All alpha proteins	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Beta chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
B	d3m2vb1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase alpha and beta chain N-terminal domain	Beta chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
E	d3m2ve2	All alpha proteins	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	Beta chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
E	d3m2ve1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase alpha and beta chain N-terminal domain	Beta chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
C	d3m2vc_	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase gamma chain	Methyl-coenzyme M reductase gamma chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)
F	d3m2vf_	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase gamma chain	Methyl-coenzyme M reductase gamma chain	(Methanothermobacter marburgensis str. Marburg ) [TaxId: 79929 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	8033121	3000812	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Methyl-coenzyme M reductase subunits	8033123	3001305	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	8033121	3000812	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Methyl-coenzyme M reductase subunits	8033123	3001305	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	8033109	3000812	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Methyl-coenzyme M reductase subunits	8033111	3001305	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Methyl-coenzyme M reductase alpha and beta chain C-terminal domain	8033109	3000812	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Methyl-coenzyme M reductase subunits	8033111	3001305	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Methyl-coenzyme M reductase subunits	8033112	3001305	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Methyl-coenzyme M reductase subunits	8033112	3001305	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	MCR_alpha	e3m2vA1	A: alpha bundles	X: Methyl-coenzyme M reductase alpha and beta chain-C (From Topology)	H: Methyl-coenzyme M reductase alpha and beta chain-C (From Topology)	T: Methyl-coenzyme M reductase alpha and beta chain-C	F: MCR_alpha	ECOD (1.6)
A	MCR_alpha_N	e3m2vA2	A: a+b two layers	X: Alpha-beta plaits	H: Methyl-coenzyme M reductase subunits (From Topology)	T: Methyl-coenzyme M reductase subunits	F: MCR_alpha_N	ECOD (1.6)
D	MCR_alpha	e3m2vD1	A: alpha bundles	X: Methyl-coenzyme M reductase alpha and beta chain-C (From Topology)	H: Methyl-coenzyme M reductase alpha and beta chain-C (From Topology)	T: Methyl-coenzyme M reductase alpha and beta chain-C	F: MCR_alpha	ECOD (1.6)
D	MCR_alpha_N	e3m2vD2	A: a+b two layers	X: Alpha-beta plaits	H: Methyl-coenzyme M reductase subunits (From Topology)	T: Methyl-coenzyme M reductase subunits	F: MCR_alpha_N	ECOD (1.6)
B	MCR_beta	e3m2vB1	A: alpha bundles	X: Methyl-coenzyme M reductase alpha and beta chain-C (From Topology)	H: Methyl-coenzyme M reductase alpha and beta chain-C (From Topology)	T: Methyl-coenzyme M reductase alpha and beta chain-C	F: MCR_beta	ECOD (1.6)
B	MCR_beta_N	e3m2vB2	A: a+b two layers	X: Alpha-beta plaits	H: Methyl-coenzyme M reductase subunits (From Topology)	T: Methyl-coenzyme M reductase subunits	F: MCR_beta_N	ECOD (1.6)
E	MCR_beta	e3m2vE1	A: alpha bundles	X: Methyl-coenzyme M reductase alpha and beta chain-C (From Topology)	H: Methyl-coenzyme M reductase alpha and beta chain-C (From Topology)	T: Methyl-coenzyme M reductase alpha and beta chain-C	F: MCR_beta	ECOD (1.6)
E	MCR_beta_N	e3m2vE2	A: a+b two layers	X: Alpha-beta plaits	H: Methyl-coenzyme M reductase subunits (From Topology)	T: Methyl-coenzyme M reductase subunits	F: MCR_beta_N	ECOD (1.6)
C	MCR_gamma	e3m2vC1	A: a+b two layers	X: Alpha-beta plaits	H: Methyl-coenzyme M reductase subunits (From Topology)	T: Methyl-coenzyme M reductase subunits	F: MCR_gamma	ECOD (1.6)
F	MCR_gamma	e3m2vF1	A: a+b two layers	X: Alpha-beta plaits	H: Methyl-coenzyme M reductase subunits (From Topology)	T: Methyl-coenzyme M reductase subunits	F: MCR_gamma	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.390.10	Alpha Beta	Alpha-Beta Complex	Methyl-coenzyme M Reductase	Chain A, domain 1	CATH (4.3.0)
A	3.30.70.470	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	1.20.840.10	Mainly Alpha	Up-down Bundle	Methyl-coenzyme M Reductase	Chain B, domain 2	CATH (4.3.0)
D	3.90.390.10	Alpha Beta	Alpha-Beta Complex	Methyl-coenzyme M Reductase	Chain A, domain 1	CATH (4.3.0)
D	3.30.70.470	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	1.20.840.10	Mainly Alpha	Up-down Bundle	Methyl-coenzyme M Reductase	Chain B, domain 2	CATH (4.3.0)
B	1.20.840.10	Mainly Alpha	Up-down Bundle	Methyl-coenzyme M Reductase	Chain B, domain 2	CATH (4.3.0)
B	3.30.70.470	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
E	1.20.840.10	Mainly Alpha	Up-down Bundle	Methyl-coenzyme M Reductase	Chain B, domain 2	CATH (4.3.0)
E	3.30.70.470	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	3.90.320.20	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)
F	3.90.320.20	Alpha Beta	Alpha-Beta Complex	Lambda Exonuclease	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D	PF02745	Methyl-coenzyme M reductase alpha subunit, N-terminal domain (MCR_alpha_N)	Methyl-coenzyme M reductase alpha subunit, N-terminal domain	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active ...	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites [1]. The N-terminal domain has a ferredoxin-like fold.	Domain
A, D	PF02249	Methyl-coenzyme M reductase alpha subunit, C-terminal domain (MCR_alpha)	Methyl-coenzyme M reductase alpha subunit, C-terminal domain	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active ...	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta (Pfam:PF02241), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites [1]. The C-terminal domain is comprised of an all-alpha multi-helical bundle.	Domain
B, E	PF02241	Methyl-coenzyme M reductase beta subunit, C-terminal domain (MCR_beta)	Methyl-coenzyme M reductase beta subunit, C-terminal domain	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (this family), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active ...	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (this family), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites [1]. The C-terminal domain of MCR beta has an all-alpha fold with buried central helix.	Domain
B, E	PF02783	Methyl-coenzyme M reductase beta subunit, N-terminal domain (MCR_beta_N)	Methyl-coenzyme M reductase beta subunit, N-terminal domain	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (this family), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active ...	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (this family), and 2 gamma (Pfam:PF02240) subunits with two identical nickel porphinoid active sites [1]. The N-terminal domain has an alpha/beta ferredoxin-like fold.	Domain
C, F	PF02240	Methyl-coenzyme M reductase gamma subunit (MCR_gamma)	Methyl-coenzyme M reductase gamma subunit	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (Pfam:PF02241), and 2 gamma (this family) subunits with two identical nickel porphinoid activ ...	Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (Pfam:PF02249), 2 beta (Pfam:PF02241), and 2 gamma (this family) subunits with two identical nickel porphinoid active sites [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, D	Methyl-coenzyme M reductase I subunit alpha	coenzyme-B sulfoethylthiotransferase activity alkylthioltransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity cation binding ion binding binding metal ion binding small molecule binding	cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process 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 cellular alkane metabolic process methanogenesis metabolic process cellular process cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process 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 cellular alkane metabolic process methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	intracellular anatomical structure cytoplasm cellular anatomical entity
B, E	Methyl-coenzyme M reductase I subunit beta	coenzyme-B sulfoethylthiotransferase activity alkylthioltransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity	cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process 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 cellular alkane metabolic process methanogenesis metabolic process cellular process cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process 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 cellular alkane metabolic process methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	intracellular anatomical structure cytoplasm cellular anatomical entity
C, F	Methyl-coenzyme M reductase I subunit gamma	coenzyme-B sulfoethylthiotransferase activity alkylthioltransferase activity transferase activity, transferring sulphur-containing groups transferase activity catalytic activity	cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process 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 cellular alkane metabolic process methanogenesis metabolic process cellular process cellular respiration energy derivation by oxidation of organic compounds cellular biosynthetic process cellular metabolic process 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 cellular alkane metabolic process methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	intracellular anatomical structure cytoplasm cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, D	IPR009047	Methyl-coenzyme M reductase, alpha subunit, C-terminal	Domain
A, D	IPR009024	Methyl-coenzyme M reductase, ferredoxin-like fold	Homologous Superfamily
A, D	IPR003183	Methyl-coenzyme M reductase, alpha subunit, N-terminal	Domain
A, D	IPR008924	Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal	Homologous Superfamily
A, D	IPR016212	Methyl coenzyme M reductase, alpha subunit	Family
A, D	IPR015823	Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2	Homologous Superfamily
A, D	IPR015811	Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 1	Homologous Superfamily
B, E	IPR009024	Methyl-coenzyme M reductase, ferredoxin-like fold	Homologous Superfamily
B, E	IPR022680	Methyl-coenzyme M reductase, beta subunit, N-terminal	Domain
B, E	IPR008924	Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal	Homologous Superfamily
B, E	IPR015823	Methyl-coenzyme M reductase, alpha subunit, N-terminal subdomain 2	Homologous Superfamily
B, E	IPR003179	Methyl-coenzyme M reductase, beta subunit	Family
B, E	IPR022679	Methyl-coenzyme M reductase, beta subunit, C-terminal	Domain
C, F	IPR009024	Methyl-coenzyme M reductase, ferredoxin-like fold	Homologous Superfamily
C, F	IPR003178	Methyl-coenzyme M reductase, gamma subunit	Family
C, F	IPR036994	Methyl-coenzyme M reductase, gamma subunit superfamily	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, D	AGM	Parent Component: ARG RESID: AA0272 PSI-MOD : 5-methyl-L-arginine MOD:00277
A, D	GL3	Parent Component: GLY RESID: AA0272 , AA0265 PSI-MOD : 5-methyl-L-arginine MOD:00277 , 1-thioglycine (internal) MOD:00270 , 1-thioglycine (C-terminal) MOD:01623
A, D	MGN	Parent Component: GLN RESID: AA0272 , AA0265 , AA0273 PSI-MOD : 5-methyl-L-arginine MOD:00277 , 1-thioglycine (internal) MOD:00270 , 1-thioglycine (C-terminal) MOD:01623 , 2-methyl-L-glutamine MOD:00278
A, D	MHS	Parent Component: HIS RESID: AA0272 , AA0265 , AA0273 , AA0073 PSI-MOD : 5-methyl-L-arginine MOD:00277 , 1-thioglycine (internal) MOD:00270 , 1-thioglycine (C-terminal) MOD:01623 , 2-methyl-L-glutamine MOD:00278 , 3'-methyl-L-histidine MOD:00082
A, D	SMC	Parent Component: CYS RESID: AA0272 , AA0265 , AA0273 , AA0073 , AA0234 PSI-MOD : 5-methyl-L-arginine MOD:00277 , 1-thioglycine (internal) MOD:00270 , 1-thioglycine (C-terminal) MOD:01623 , 2-methyl-L-glutamine MOD:00278 , 3'-methyl-L-histidine MOD:00082 , S-methyl-L-cysteine MOD:00239

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.