6YY3 | pdb_00006yy3

XFEL structure of the Soluble methane monooxygenase hydroxylase and regulatory subunit complex, from Methylosinus trichosporium OB3b, t=0 diferrous state prior to oxygen activation

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 [auth G]	d6yy3g_	Alpha and beta proteins (a+b)	Monooxygenase (hydroxylase) regulatory protein	Monooxygenase (hydroxylase) regulatory protein	Monooxygenase (hydroxylase) regulatory protein	automated matches	(Methylosinus trichosporium OB3b ) [TaxId: 595536 ],	SCOPe (2.08)
C [auth F]	d6yy3f_	All alpha proteins	Open three-helical up-and-down bundle	Methane monooxygenase hydrolase, gamma subunit	Methane monooxygenase hydrolase, gamma subunit	automated matches	(Methylosinus trichosporium OB3b ) [TaxId: 595536 ],	SCOPe (2.08)
B [auth D]	d6yy3d_	All alpha proteins	Ferritin-like	Ferritin-like	Ribonucleotide reductase-like	automated matches	(Methylosinus trichosporium OB3b ) [TaxId: 595536 ],	SCOPe (2.08)
A [auth B]	d6yy3b_	All alpha proteins	Ferritin-like	Ferritin-like	Ribonucleotide reductase-like	automated matches	(Methylosinus trichosporium OB3b ) [TaxId: 595536 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth G]	SCOP2B Superfamily	Monooxygenase (hydroxylase) regulatory protein	8096654	3000674	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	Methane monooxygenase hydrolase, gamma subunit	8096406	3001468	SCOP2B (2022-06-29)
B [auth D]	SCOP2B Superfamily	Ferritin-like	8037031	3001658	SCOP2B (2022-06-29)
A [auth B]	SCOP2 Family	Ribonucleotide reductase-like	8096407	4000846	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	Ferritin-like	8096408	3001658	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 [auth G]	MmoB_DmpM	e6yy3G1	A: a+b two layers	X: Alpha-beta plaits	H: Monooxygenase (hydroxylase) regulatory protein (From Topology)	T: Monooxygenase (hydroxylase) regulatory protein	F: MmoB_DmpM	ECOD (1.6)
C [auth F]	MeMO_Hyd_G	e6yy3F1	A: alpha arrays	X: Methane monooxygenase hydrolase gamma subunit-like	H: Methane monooxygenase hydrolase gamma subunit (From Topology)	T: Methane monooxygenase hydrolase gamma subunit	F: MeMO_Hyd_G	ECOD (1.6)
B [auth D]	Phenol_Hydrox	e6yy3D1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Phenol_Hydrox	ECOD (1.6)
A [auth B]	Phenol_Hydrox	e6yy3B1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: Ferritin/Heme oxygenase	T: Heme oxygenase/Ribonucleotide reductase	F: Phenol_Hydrox	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth G]	PF02406	MmoB/DmpM family (MmoB_DmpM)	MmoB/DmpM family	This family consists of monooxygenase components such as MmoB methane monooxygenase (EC:1.14.13.25) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilises inte ...	This family consists of monooxygenase components such as MmoB methane monooxygenase (EC:1.14.13.25) regulatory protein B. When MmoB is present at low concentration it converts methane monooxygenase from an oxidase to a hydroxylase and stabilises intermediates required for the activation of dioxygen [1]. Also found in this family is DmpM or Phenol hydroxylase (EC:1.14.13.7) protein component P2, this protein lacks redox co-factors and is required for optimal turnover of Phenol hydroxylase [3].	Domain
C [auth F]	PF02964	Methane monooxygenase, hydrolase gamma chain (MeMO_Hyd_G)	Methane monooxygenase, hydrolase gamma chain		Domain
B [auth D]	PF02332	Methane/Phenol/Alkene Hydroxylase (Phenol_Hydrox)	Methane/Phenol/Alkene Hydroxylase	This protein family includes several components of multicomponent enzyme systems predominantly found in Proteobacteria and Actinobacteria, including subunits alpha and beta of a methane monooxygenase and an alkene monooxygenase system, small and larg ...	This protein family includes several components of multicomponent enzyme systems predominantly found in Proteobacteria and Actinobacteria, including subunits alpha and beta of a methane monooxygenase and an alkene monooxygenase system, small and large subunits of propane 2-monooxygenase system and P1 protein of phenol hydroxylase [1-4].	Domain
A [auth B]	PF02332	Methane/Phenol/Alkene Hydroxylase (Phenol_Hydrox)	Methane/Phenol/Alkene Hydroxylase	This protein family includes several components of multicomponent enzyme systems predominantly found in Proteobacteria and Actinobacteria, including subunits alpha and beta of a methane monooxygenase and an alkene monooxygenase system, small and larg ...	This protein family includes several components of multicomponent enzyme systems predominantly found in Proteobacteria and Actinobacteria, including subunits alpha and beta of a methane monooxygenase and an alkene monooxygenase system, small and large subunits of propane 2-monooxygenase system and P1 protein of phenol hydroxylase [1-4].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth G]	Methane monooxygenase regulatory protein B	monooxygenase activity oxidoreductase activity catalytic activity	-	-
C [auth F]	Methane monooxygenase	oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen methane monooxygenase [NAD(P)H] activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity	alkane metabolic process methane metabolic process metabolic process cellular process hydrocarbon metabolic process	-
B [auth D]	Methane monooxygenase component A alpha chain	oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen methane monooxygenase [NAD(P)H] activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity cation binding ion binding binding metal ion binding small molecule binding	small molecule metabolic process metabolic process cellular process one-carbon metabolic process	-
A [auth B]	Methane monooxygenase	oxidoreductase activity monooxygenase activity oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen catalytic activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth G]	IPR036889	Monooxygenase component MmoB/DmpM superfamily	Homologous Superfamily
D [auth G]	IPR003454	Monooxygenase component MmoB/DmpM	Family
D [auth G]	IPR054955	Methane monooxygenase regulatory protein B	Family
C [auth F]	IPR015952	Methane monooxygenase, gamma chain, domain 1	Homologous Superfamily
C [auth F]	IPR054953	Methane monooxygenase component A gamma chain	Family
C [auth F]	IPR015953	Methane monooxygenase, gamma chain, domain 2	Homologous Superfamily
C [auth F]	IPR036123	Methane monooxygenase, gamma chain superfamily	Homologous Superfamily
C [auth F]	IPR004222	Methane monooxygenase, gamma chain	Family
B [auth D]	IPR009078	Ferritin-like superfamily	Homologous Superfamily
B [auth D]	IPR003430	Propane/methane/phenol/toluene hydroxylase	Family
B [auth D]	IPR012348	Ribonucleotide reductase-like	Homologous Superfamily
A [auth B]	IPR054956	Methane monooxygenase component A beta chain	Family
A [auth B]	IPR009078	Ferritin-like superfamily	Homologous Superfamily
A [auth B]	IPR003430	Propane/methane/phenol/toluene hydroxylase	Family
A [auth B]	IPR012078	Methane/phenol monooxygenase, hydroxylase component	Family
A [auth B]	IPR012348	Ribonucleotide reductase-like	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.