7NKG | pdb_00007nkg

Methyl-coenzyme M reductase from Methermicoccus shengliensis at 1.6-A resolution

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
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)
L	d7nkgl_	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase gamma chain	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
I	d7nkgi_	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase gamma chain	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
F	d7nkgf_	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase gamma chain	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
C	d7nkgc_	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	Methyl-coenzyme M reductase gamma chain	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
K	d7nkgk2	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	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
K	d7nkgk1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
H	d7nkgh2	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	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
H	d7nkgh1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
E	d7nkge2	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	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
E	d7nkge1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
B	d7nkgb2	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	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
B	d7nkgb1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
J	d7nkgj2	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	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
J	d7nkgj1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
G	d7nkgg2	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	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
G	d7nkgg1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
D	d7nkgd2	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	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
D	d7nkgd1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
A	d7nkga2	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	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)
A	d7nkga1	Alpha and beta proteins (a+b)	Ferredoxin-like	Methyl-coenzyme M reductase subunits	automated matches	automated matches	(Methermicoccus shengliensis DSM 18856 ) [TaxId: 1122233 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
L	MCR_gamma	e7nkgL1	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	e7nkgI1	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	e7nkgF1	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)
C	MCR_gamma	e7nkgC1	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)
K	MCR_beta	e7nkgK1	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)
K	MCR_beta_N	e7nkgK2	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	e7nkgH1	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	e7nkgH2	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	e7nkgE1	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	e7nkgE2	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)
B	MCR_beta	e7nkgB1	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	e7nkgB2	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)
J	MCR_alpha	e7nkgJ1	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)
J	MCR_alpha_N	e7nkgJ2	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	e7nkgG2	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	e7nkgG1	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	e7nkgD1	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	e7nkgD2	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)
A	MCR_alpha	e7nkgA2	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	e7nkgA1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, F, I, L	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 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 (Pfam:PF02241), and 2 gamma (this family) subunits with two identical nickel porphinoid active sites [1].	Domain
B, E, H, K	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, K	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
A, D, G, J	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, J	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L	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 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 anaerobic respiration	-
B, E, H, K	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 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 anaerobic respiration	-
A, D, G, J	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 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 anaerobic respiration	-

InterPro: Protein Family Classification InterPro Database Homepage

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

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A, D, G, J	AGM	Parent Component: ARG RESID: AA0272 PSI-MOD : 5-methyl-L-arginine MOD:00277
A, D, G, J	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, G, J	MHS	Parent Component: HIS RESID: AA0272 , AA0265 , AA0073 PSI-MOD : 5-methyl-L-arginine MOD:00277 , 1-thioglycine (internal) MOD:00270 , 1-thioglycine (C-terminal) MOD:01623 , 3'-methyl-L-histidine MOD:00082