2VCK

Structure of Phycoerythrobilin Synthase PebS from the Cyanophage P-SSM2 in Complex with the bound Substrate Biliverdin IXa

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Coproporphyrinogen III oxidase	8053220	3001418	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Coproporphyrinogen III oxidase	8053220	3001418	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Coproporphyrinogen III oxidase	8053220	3001418	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Coproporphyrinogen III oxidase	8053220	3001418	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	PF05996	e2vckA1	A: a+b three layers	X: Coproporphyrinogen III oxidase (From Topology)	H: Coproporphyrinogen III oxidase (From Topology)	T: Coproporphyrinogen III oxidase	F: PF05996	ECOD (1.6)
B	PF05996	e2vckB1	A: a+b three layers	X: Coproporphyrinogen III oxidase (From Topology)	H: Coproporphyrinogen III oxidase (From Topology)	T: Coproporphyrinogen III oxidase	F: PF05996	ECOD (1.6)
C	PF05996	e2vckC1	A: a+b three layers	X: Coproporphyrinogen III oxidase (From Topology)	H: Coproporphyrinogen III oxidase (From Topology)	T: Coproporphyrinogen III oxidase	F: PF05996	ECOD (1.6)
D	PF05996	e2vckD1	A: a+b three layers	X: Coproporphyrinogen III oxidase (From Topology)	H: Coproporphyrinogen III oxidase (From Topology)	T: Coproporphyrinogen III oxidase	F: PF05996	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.1500.20	Alpha Beta	3-Layer(aba) Sandwich	oxygen-dependent coproporphyrinogen oxidase		CATH (4.3.0)
B	3.40.1500.20	Alpha Beta	3-Layer(aba) Sandwich	oxygen-dependent coproporphyrinogen oxidase		CATH (4.3.0)
C	3.40.1500.20	Alpha Beta	3-Layer(aba) Sandwich	oxygen-dependent coproporphyrinogen oxidase		CATH (4.3.0)
D	3.40.1500.20	Alpha Beta	3-Layer(aba) Sandwich	oxygen-dependent coproporphyrinogen oxidase		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF05996	Ferredoxin-dependent bilin reductase (Fe_bilin_red)	Ferredoxin-dependent bilin reductase	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	CYANOBACTERIAL PHYCOERYTHROBILIN	cation binding transition metal ion binding ion binding binding metal ion binding cobalt ion binding small molecule binding oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor oxidoreductase activity oxidoreductase activity, acting on the CH-CH group of donors catalytic activity	phytochromobilin biosynthetic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process organic substance metabolic process tetrapyrrole biosynthetic process organic substance biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process organonitrogen compound metabolic process tetrapyrrole metabolic process phytochromobilin biosynthetic process oxoacid metabolic process cellular biosynthetic process organonitrogen compound biosynthetic process organic acid metabolic process organic acid biosynthetic process carboxylic acid biosynthetic process organic substance metabolic process tetrapyrrole biosynthetic process organic substance biosynthetic process small molecule metabolic process dicarboxylic acid biosynthetic process organonitrogen compound metabolic process tetrapyrrole metabolic process small molecule biosynthetic process cellular metabolic process dicarboxylic acid metabolic process carboxylic acid metabolic process phytochromobilin metabolic process organic cyclic compound metabolic process biosynthetic process organic cyclic compound biosynthetic process metabolic process cellular process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR009249	Ferredoxin-dependent bilin reductase	Family

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

Chains	Enzyme Name	Description	Catalytic Residues
A	phycoerythrobilin synthase M-CSA #306	Plays a role in phycoerythrobilin biosynthesis, the red pigment chromophore photosynthetically active biliproteins of a cyanophage infecting oceanic cyanobacteria of the Prochlorococcus genus. It uses a four electron reduction to carry out the reactions catalyses by EC 1.3.7.2 (15,16-dihydrobiliverdin:ferredoxin oxidoreductase) and EC 1.3.7.3 (phycoerythrobilin:ferredoxin oxidoreductase). 15,16-Dihydrobiliverdin is formed as a bound intermediate. Free 15,16-dihydrobiliverdin can also act as a substrate to form phycoerythrobilin.	Defined by 2 residues: ASP:A-105ASP:A-206 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.3.7.6 (PDB Primary Data) Search M-CSA Motif + EC 1.3.7.6

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.