5M4O

Crystal structure of hydroquinone 1,2-dioxygenase from Sphingomonas sp. TTNP3 in complex with 4-nitrophenol

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	F_UNCLASSIFIED	e5m4oA1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: F_UNCLASSIFIED	ECOD (1.6)
C	F_UNCLASSIFIED	e5m4oC1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: F_UNCLASSIFIED	ECOD (1.6)
E	F_UNCLASSIFIED	e5m4oE1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: F_UNCLASSIFIED	ECOD (1.6)
G	F_UNCLASSIFIED	e5m4oG1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: F_UNCLASSIFIED	ECOD (1.6)
B	F_UNCLASSIFIED	e5m4oB1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF18191	e5m4oB2	A: a+b two layers	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain (From Topology)	T: ssDNA-binding transcriptional regulator domain	F: PF18191	ECOD (1.6)
D	F_UNCLASSIFIED	e5m4oD2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF18191	e5m4oD1	A: a+b two layers	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain (From Topology)	T: ssDNA-binding transcriptional regulator domain	F: PF18191	ECOD (1.6)
F	F_UNCLASSIFIED	e5m4oF2	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: F_UNCLASSIFIED	ECOD (1.6)
F	PF18191	e5m4oF1	A: a+b two layers	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain (From Topology)	T: ssDNA-binding transcriptional regulator domain	F: PF18191	ECOD (1.6)
H	F_UNCLASSIFIED	e5m4oH1	A: beta sandwiches	X: jelly-roll	H: Double-stranded beta-helix (From Topology)	T: Double-stranded beta-helix	F: F_UNCLASSIFIED	ECOD (1.6)
H	PF18191	e5m4oH2	A: a+b two layers	X: ssDNA-binding transcriptional regulator domain-like	H: ssDNA-binding transcriptional regulator domain (From Topology)	T: ssDNA-binding transcriptional regulator domain	F: PF18191	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF18191	Hydroquinone 1,2-dioxygenase large subunit N-terminal (PnpCD_PnpD_N)	Hydroquinone 1,2-dioxygenase large subunit N-terminal	This is the N-terminal domain of the alpha subunit, known as PnpD, of Hydroquinone 1,2-dioxygenase (PnpCD) present in Pseudomonas sp. strain WBC-3. PnpCD is the key enzyme in the degradation pathway of pollutant para-nitrophenol (PNP). The N-terminal ...	This is the N-terminal domain of the alpha subunit, known as PnpD, of Hydroquinone 1,2-dioxygenase (PnpCD) present in Pseudomonas sp. strain WBC-3. PnpCD is the key enzyme in the degradation pathway of pollutant para-nitrophenol (PNP). The N-terminal domain residues Trp-76 and Phe-79 are indispensable in the formation of the active site pocket. The N-terminal domain also plays a vital role in formation of the heterotetrameric structure. Structural homologs of the N-terminal domain exhibit the nature to bind nucleic acids but due to the steric effect of the C-terminal domain, this N-terminal domain cannot bind nucleic acids [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Hydroquinone dioxygenase small subunit	oxidoreductase activity catalytic activity dioxygenase activity	-	-
B, D, F, H	Hydroquinone dioxygenase large subunit	oxidoreductase activity catalytic activity dioxygenase activity	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H	IPR011051	RmlC-like cupin domain superfamily	Homologous Superfamily
B, D, F, H	IPR040908	Hydroquinone 1,2-dioxygenase large subunit, N-terminal	Domain

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 R01GM133198.