1DII

CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE AT 2.5 A RESOLUTION

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
Structure Motif: Primary M-CSA Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1diia1	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	Vanillyl-alcohol oxidase-like	Flavoprotein subunit of p-cresol methylhydroxylase	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
A	d1diia2	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	Flavoprotein subunit of p-cresol methylhydroxylase	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C [auth B]	d1diib1	Alpha and beta proteins (a+b)	Ferredoxin-like	FAD-linked oxidases, C-terminal domain	Vanillyl-alcohol oxidase-like	Flavoprotein subunit of p-cresol methylhydroxylase	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
C [auth B]	d1diib2	Alpha and beta proteins (a+b)	FAD-binding/transporter-associated domain-like	FAD-binding/transporter-associated domain-like	FAD-linked oxidases, N-terminal domain	Flavoprotein subunit of p-cresol methylhydroxylase	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
B [auth C]	d1diic_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	p-Cresol methylhydroxylase, cytochrome c subunit	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)
D	d1diid_	All alpha proteins	Cytochrome c	Cytochrome c	monodomain cytochrome c	p-Cresol methylhydroxylase, cytochrome c subunit	(Pseudomonas putida ) [TaxId: 303 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	FAD-linked oxidases C-terminal domain-like	8033320	3001317	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8033323	3000913	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	FAD-linked oxidases C-terminal domain-like	8033320	3001317	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	FAD-binding/transporter-associated domain-like	8033323	3000913	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Cytochrome c	8033316	3000815	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cytochrome c	8033316	3000815	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	FAD-oxidase_C	e1diiA1	A: a+b two layers	X: Alpha-beta plaits	H: FAD-linked oxidases, C-terminal domain (From Topology)	T: FAD-linked oxidases, C-terminal domain	F: FAD-oxidase_C	ECOD (1.6)
A	FAD_binding_4	e1diiA2	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_4	ECOD (1.6)
C [auth B]	FAD-oxidase_C	e1diiB1	A: a+b two layers	X: Alpha-beta plaits	H: FAD-linked oxidases, C-terminal domain (From Topology)	T: FAD-linked oxidases, C-terminal domain	F: FAD-oxidase_C	ECOD (1.6)
C [auth B]	FAD_binding_4	e1diiB2	A: a+b complex topology	X: FAD-binding domain-like	H: FAD-binding domain (From Topology)	T: FAD-binding domain	F: FAD_binding_4	ECOD (1.6)
B [auth C]	Cytochrome_CBB3	e1diiC1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)
D	Cytochrome_CBB3	e1diiD1	A: alpha arrays	X: Cytochrome c-like	H: Cytochrome c (From Topology)	T: Cytochrome c	F: Cytochrome_CBB3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.462.10	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
A	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
A	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
A	1.10.45.10	Mainly Alpha	Orthogonal Bundle	Vanillyl-alcohol Oxidase	Chain A, domain 4	CATH (4.3.0)
C [auth B]	3.40.462.10	Alpha Beta	3-Layer(aba) Sandwich	Vanillyl-alcohol Oxidase	Chain A, domain 3	CATH (4.3.0)
C [auth B]	3.30.43.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 2	CATH (4.3.0)
C [auth B]	3.30.465.10	Alpha Beta	2-Layer Sandwich	Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase	domain 3	CATH (4.3.0)
C [auth B]	1.10.45.10	Mainly Alpha	Orthogonal Bundle	Vanillyl-alcohol Oxidase	Chain A, domain 4	CATH (4.3.0)
B [auth C]	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)
D	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF02913	FAD linked oxidases, C-terminal domain (FAD-oxidase_C)	FAD linked oxidases, C-terminal domain	This domain has a ferredoxin-like fold.	Domain
A, C [auth B]	PF01565	FAD binding domain (FAD_binding_4)	FAD binding domain	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, call ...	This family consists of various enzymes that use FAD as a co-factor, most of the enzymes are similar to oxygen oxidoreductase. One of the enzymes Vanillyl-alcohol oxidase (VAO) has a solved structure, the alignment includes the FAD binding site, called the PP-loop, between residues 99-110 [1]. The FAD molecule is covalently bound in the known structure, however the residue that links to the FAD is not in the alignment. VAO catalyses the oxidation of a wide variety of substrates, ranging form aromatic amines to 4-alkylphenols. Other members of this family include D-lactate dehydrogenase, this enzyme catalyses the conversion of D-lactate to pyruvate using FAD as a co-factor; mitomycin radical oxidase, this enzyme oxidises the reduced form of mitomycins and is involved in mitomycin resistance. This family includes MurB an UDP-N-acetylenolpyruvoylglucosamine reductase enzyme EC:1.1.1.158. This enzyme is involved in the biosynthesis of peptidoglycan [2].	Domain
B [auth C], D	PF13442	Cytochrome C oxidase, cbb3-type, subunit III (Cytochrome_CBB3)	Cytochrome C oxidase, cbb3-type, subunit III	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	P-CRESOL METHYLHYDROXYLASE	oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors lactate dehydrogenase activity D-lactate dehydrogenase activity catalytic activity oxidoreductase activity, acting on CH or CH2 groups 4-cresol dehydrogenase (hydroxylating) activity D-lactate dehydrogenase (cytochrome) activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors lactate dehydrogenase activity D-lactate dehydrogenase activity catalytic activity oxidoreductase activity, acting on CH or CH2 groups 4-cresol dehydrogenase (hydroxylating) activity D-lactate dehydrogenase (cytochrome) activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding organic cyclic compound binding anion binding nucleotide binding heterocyclic compound binding small molecule binding	catabolic process oxoacid metabolic process lactate catabolic process organic hydroxy compound metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process lactate metabolic process cellular catabolic process monocarboxylic acid catabolic process organic hydroxy compound catabolic process carboxylic acid catabolic process metabolic process catabolic process oxoacid metabolic process lactate catabolic process organic hydroxy compound metabolic process cellular metabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process lactate metabolic process cellular catabolic process monocarboxylic acid catabolic process organic hydroxy compound catabolic process carboxylic acid catabolic process metabolic process small molecule metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process	-
B [auth C], D	P-CRESOL METHYLHYDROXYLASE	binding organic cyclic compound binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR016167	FAD-binding, type PCMH, subdomain 1	Homologous Superfamily
A, C [auth B]	IPR016164	FAD-linked oxidase-like, C-terminal	Homologous Superfamily
A, C [auth B]	IPR016170	Cytokinin dehydrogenase, C-terminal domain superfamily	Homologous Superfamily
A, C [auth B]	IPR006094	FAD linked oxidase, N-terminal	Domain
A, C [auth B]	IPR004113	FAD-binding oxidoreductase/transferase, type 4, C-terminal	Domain
A, C [auth B]	IPR016166	FAD-binding domain, PCMH-type	Domain
A, C [auth B]	IPR016171	Vanillyl-alcohol oxidase, C-terminal subdomain 2	Homologous Superfamily
A, C [auth B]	IPR036318	FAD-binding, type PCMH-like superfamily	Homologous Superfamily
A, C [auth B]	IPR016169	FAD-binding, type PCMH, subdomain 2	Homologous Superfamily
B [auth C], D	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B [auth C], D	IPR009056	Cytochrome c-like domain	Domain

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A, B [auth C]	4-cresol dehydrogenase (hydroxylating) M-CSA #141	4-Cresol dehydrogenase is a flavocytochrome c protein. It is the first enzyme in the protocatechuate metabolic pathway and is responsible for the degradation of toxic phenol p-cresol. The active site is buried deeply in the enzyme's interior. The route of substrate access has been shown to follow a swinging gate mechanism.	Defined by 12 residues: ASP:A-167GLU:A-177GLU:A-286TYR:A-367GLU:A-380TYR:A-384HIS:A-436TYR:A-473ARG:A-474ARG:A-512ALA:B-49 [auth C-649]MET:B-50 [auth C-650] \| Explore in 3D: M-CSA Motif Definition Up to 10 residues are supported for Structure Motif searching, this motif has 12 residues. EC: 1.17.99.1 (PDB Primary Data) EC: 1.17.9.1 (UniProt)

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.