3TGV

Crystal structure of HutZ,the heme storsge protein from Vibrio cholerae

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3tgva1	All beta proteins	Split barrel-like	FMN-binding split barrel	automated matches	automated matches	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
A	d3tgva3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
A	d3tgva2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
B	d3tgvb1	All beta proteins	Split barrel-like	FMN-binding split barrel	automated matches	automated matches	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
B	d3tgvb3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
B	d3tgvb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
C	d3tgvc1	All beta proteins	Split barrel-like	FMN-binding split barrel	automated matches	automated matches	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
C	d3tgvc3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
C	d3tgvc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
D	d3tgvd1	All beta proteins	Split barrel-like	FMN-binding split barrel	automated matches	automated matches	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
D	d3tgvd3	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)
D	d3tgvd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Vibrio cholerae O395 ) [TaxId: 345073 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	PNP-oxidase like	8065373	4002129	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	FMN-binding split barrel	8065374	3000856	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	FMN-binding split barrel	8065374	3000856	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FMN-binding split barrel	8065374	3000856	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	FMN-binding split barrel	8065374	3000856	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	Pyrid_oxidase_2	e3tgvA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Pyrid_oxidase_2	ECOD (1.6)
B	Pyrid_oxidase_2	e3tgvB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Pyrid_oxidase_2	ECOD (1.6)
C	Pyrid_oxidase_2	e3tgvC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Pyrid_oxidase_2	ECOD (1.6)
D	Pyrid_oxidase_2	e3tgvD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: Pyrid_oxidase_2	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
B	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
C	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
D	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01243	Pyridoxamine 5'-phosphate oxidase (PNPOx_N)	Pyridoxamine 5'-phosphate oxidase	This entry includes pyridoxamine 5'-phosphate oxidases, FMN flavoproteins that catalyse the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of ...	This entry includes pyridoxamine 5'-phosphate oxidases, FMN flavoproteins that catalyse the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP). This reaction serves as the terminal step in the de novo biosynthesis of PLP in Escherichia coli and as a part of the salvage pathway of this coenzyme in both E. coli and mammalian cells [1-5]. The binding sites for FMN and for substrate have been highly conserved throughout evolution. In some species, the coenzyme F420 may perform the FMN role [7]. This entry represents the N-terminal segment of these proteins, which is involved in FMN binding when they form the dimer [5]. In human PNPO, it has been shown that this region contains some of the residues that constitute the PLP allosteric site which regulates its activity [4]. The C-terminal region of these proteins (Pfam:PF10590) is involved in dimerisation and also contributes some residues to the PLP allosteric site. Some of the members included in this entry are involved in phenazine biosynthesis [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Heme-binding protein HutZ	organic acid binding binding ion binding anion binding coenzyme F420 binding carboxylic acid binding heterocyclic compound binding carbohydrate derivative binding small molecule binding oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity	-	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR012349	FMN-binding split barrel	Homologous Superfamily
A, B, C, D	IPR014419	Heme utilization protein HutZ	Family
A, B, C, D	IPR011576	Pyridoxamine 5'-phosphate oxidase, N-terminal	Domain
A, B, C, D	IPR052019	F420H(2)-dependent biliverdin reductase/Heme oxygenase	Family

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.