1DII | pdb_00001dii

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
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)
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)
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)
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)
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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cytochrome c	8033316	3000815	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Cytochrome c	8033316	3000815	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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	MgsA_C	e1diiD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: MgsA_C	ECOD (v294.1)
B [auth C]	MgsA_C	e1diiC1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	T: alpha-2-Macroglobulin receptor associated protein (RAP) domain 1	F: MgsA_C	ECOD (v294.1)
C [auth B]	Propep_M14	e1diiB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Propep_M14	ECOD (v294.1)
C [auth B]	LRR_6,LRR_RI_capping	e1diiB2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.1)
A	Propep_M14	e1diiA1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: Rpp14/Pop5-like	T: Rpp14/Pop5-like	F: Propep_M14	ECOD (v294.1)
A	LRR_6,LRR_RI_capping	e1diiA2	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: LRR_6,LRR_RI_capping	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.10.760.10	Mainly Alpha	Orthogonal Bundle	Cytochrome Bc1 Complex	Chain D, domain 2	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)
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)
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)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D	P-CRESOL METHYLHYDROXYLASE	binding tetrapyrrole binding heme binding electron transfer activity cation binding ion binding metal ion binding small molecule binding	-	-
A, C [auth B]	P-CRESOL METHYLHYDROXYLASE	oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups 4-cresol dehydrogenase (hydroxylating) activity catalytic activity D-lactate dehydrogenase (cytochrome) activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor (2R)-oxo-acid reductase activity oxidoreductase activity, acting on CH-OH group of donors lactate dehydrogenase activity D-lactate dehydrogenase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups 4-cresol dehydrogenase (hydroxylating) activity catalytic activity D-lactate dehydrogenase (cytochrome) activity oxidoreductase activity, acting on the CH-OH group of donors, cytochrome as acceptor (2R)-oxo-acid reductase activity oxidoreductase activity, acting on CH-OH group of donors lactate dehydrogenase activity D-lactate dehydrogenase activity FAD binding flavin adenine dinucleotide binding binding nucleoside phosphate binding ion binding anion binding nucleotide binding heterocyclic compound binding small molecule binding (2R)-2-hydroxyacid dehydrogenase (NAD+) activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor D-lactate dehydrogenase (NAD+) activity	catabolic process oxoacid metabolic process lactate catabolic process carboxylic acid metabolic process organic acid metabolic process organic acid catabolic process lactate metabolic process monocarboxylic acid catabolic process carboxylic acid catabolic process small molecule metabolic process metabolic process cellular process monocarboxylic acid metabolic process small molecule catabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR036909	Cytochrome c-like domain superfamily	Homologous Superfamily
B [auth C], D	IPR009056	Cytochrome c-like domain	Domain
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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.