3SQG

Crystal structure of a methyl-coenzyme M reductase purified from Black Sea mats

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	d3sqga2	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	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
A	d3sqga1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
G	d3sqgg2	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	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
G	d3sqgg1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
D	d3sqgd2	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	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
D	d3sqgd1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
B	d3sqgb2	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	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
B	d3sqgb1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
E	d3sqge2	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	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
E	d3sqge1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
H	d3sqgh2	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	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)
H	d3sqgh1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(uncultured archaeon ) [TaxId: 115547 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2 Family	Methyl-coenzyme M reductase gamma chain	8073482	4001330	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Methyl-coenzyme M reductase subunits	8073483	3001305	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Methyl-coenzyme M reductase subunits	8073483	3001305	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Methyl-coenzyme M reductase subunits	8073483	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	e3sqgA2	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	e3sqgA1	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)
G	MCR_alpha	e3sqgG1	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)
G	MCR_alpha_N	e3sqgG2	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	e3sqgD1	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	e3sqgD2	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	e3sqgB1	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	e3sqgB2	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	e3sqgE1	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	e3sqgE2	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)
H	MCR_beta	e3sqgH1	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)
H	MCR_beta_N	e3sqgH2	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	e3sqgC1	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	e3sqgF1	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)
I	MCR_gamma	e3sqgI1	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)
G	3.90.390.10	Alpha Beta	Alpha-Beta Complex	Methyl-coenzyme M Reductase	Chain A, domain 1	CATH (4.3.0)
G	3.30.70.470	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
G	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)
H	1.20.840.10	Mainly Alpha	Up-down Bundle	Methyl-coenzyme M Reductase	Chain B, domain 2	CATH (4.3.0)
H	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)
I	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, G	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, G	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, H	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, H	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, I	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, G	Methyl coenzyme M reductase, alpha subunit	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 organic substance metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process organic substance biosynthetic process methanogenesis 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 organic substance metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process organic substance biosynthetic process methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
B, E, H	Methyl-coenzyme M reductase, beta subunit	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 organic substance metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process organic substance biosynthetic process methanogenesis 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 organic substance metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process organic substance biosynthetic process methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-
C, F, I	Methyl-coenzyme M reductase, gamma subunit	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 organic substance metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process organic substance biosynthetic process methanogenesis 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 organic substance metabolic process biosynthetic process energy derivation by oxidation of reduced inorganic compounds cellular alkane metabolic process organic substance biosynthetic process methanogenesis metabolic process cellular process hydrocarbon biosynthetic process anaerobic respiration	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, D, G	0AF	Parent Component: TRP RESID: AA0520 PSI-MOD : 7'-hydroxy-L-tryptophan MOD:01664
A, D, G	GL3	Parent Component: GLY RESID: AA0520 , AA0265 PSI-MOD : 7'-hydroxy-L-tryptophan MOD:01664 , 1-thioglycine (internal) MOD:00270 , 1-thioglycine (C-terminal) MOD:01623
A, D, G	MHO	Parent Component: MET RESID: AA0520 , AA0265
A, D, G	MHS	Parent Component: HIS RESID: AA0520 , AA0265 , AA0073 PSI-MOD : 7'-hydroxy-L-tryptophan MOD:01664 , 1-thioglycine (internal) MOD:00270 , 1-thioglycine (C-terminal) MOD:01623 , 3'-methyl-L-histidine MOD:00082

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.