Annotations: 5JAB

Structure of the biliverdin reductase Rv2074 from Mycobacterium tuberculosis in complex with F420

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)
D	d5jabd_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
C	d5jabc_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
B	d5jabb_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)
A	d5jaba_	All beta proteins	Split barrel-like	FMN-binding split barrel	PNP-oxidase like	automated matches	(Mycobacterium tuberculosis H37Rv ) [TaxId: 83332 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	FMN-binding split barrel	8037328	3000856	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	FMN-binding split barrel	8037328	3000856	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	FMN-binding split barrel	8037328	3000856	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	FMN-binding split barrel	8037328	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)
D		e5jabD1	A: beta barrels	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F:	ECOD (v294.2)
C		e5jabC1	A: beta barrels	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F:	ECOD (v294.2)
B		e5jabB1	A: beta barrels	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F:	ECOD (v294.2)
A		e5jabA1	A: beta barrels	X: MocoBD/DmpA-related	H: MocoBD/DmpA-related	T: Retrovirus capsid protein-C	F:	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	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)
B	2.30.110.10	Mainly Beta	Roll	Pnp Oxidase	Chain A	CATH (4.3.0)
A	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	Biliverdin reductase Rv2074	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity organic acid binding ion binding anion binding coenzyme F420 binding carboxylic acid binding heterocyclic compound binding carbohydrate derivative binding small molecule binding oxidoreductase activity identical protein binding protein binding binding protein homodimerization activity protein dimerization activity organic acid 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	-	cell surface cellular anatomical structure external encapsulating structure extracellular region cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR019920	F420-binding domain, putative	Domain
A, B, C, D	IPR012349	FMN-binding split barrel	Homologous Superfamily
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

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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.