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PDBsum entry 2vck

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protein ligands Protein-protein interface(s) links
Oxidoreductase PDB id
2vck
Jmol
Contents
Protein chains
208 a.a. *
Ligands
BLA ×4
Waters ×575
* Residue conservation analysis
PDB id:
2vck
Name: Oxidoreductase
Title: Structure of phycoerythrobilin synthase pebs from the cyanophage p-ssm2 in complex with the bound substrate biliverdin ixa
Structure: Cyanobacterial phycoerythrobilin. Chain: a, b, c, d. Synonym: phycobilin reductase, cyanophage phycoerythrobilin synthase pebs. Engineered: yes
Source: Prochlorococcus phage p-ssm2. Organism_taxid: 268746. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Resolution:
1.80Å     R-factor:   0.187     R-free:   0.225
Authors: T.Dammeyer,E.Hofmann,N.Frankenberg-Dinkel
Key ref:
T.Dammeyer et al. (2008). Phycoerythrobilin Synthase (PebS) of a Marine Virus: CRYSTAL STRUCTURES OF THE BILIVERDIN COMPLEX AND THE SUBSTRATE-FREE FORM. J Biol Chem, 283, 27547-27554. PubMed id: 18662988 DOI: 10.1074/jbc.M803765200
Date:
25-Sep-07     Release date:   05-Aug-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q58MU6  (PEBS_BPPRM) -  Phycoerythrobilin synthase
Seq:
Struc:
233 a.a.
208 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.1.3.7.6  - Phycoerythrobilin synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: (3Z)-phycoerythrobilin + 2 oxidized ferredoxin = biliverdin IX-alpha + 2 reduced ferredoxin
(3Z)-phycoerythrobilin
Bound ligand (Het Group name = BLA)
corresponds exactly
+ 2 × oxidized ferredoxin
= biliverdin IX-alpha
+ 2 × reduced ferredoxin
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   2 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.M803765200 J Biol Chem 283:27547-27554 (2008)
PubMed id: 18662988  
 
 
Phycoerythrobilin Synthase (PebS) of a Marine Virus: CRYSTAL STRUCTURES OF THE BILIVERDIN COMPLEX AND THE SUBSTRATE-FREE FORM.
T.Dammeyer, E.Hofmann, N.Frankenberg-Dinkel.
 
  ABSTRACT  
 
The reddish purple open chain tetrapyrrole pigment phycoerythrobilin (PEB; A(lambdamax) approximately 550 nm) is an essential chromophore of the light-harvesting phycobiliproteins of most cyanobacteria, red algae, and cryptomonads. The enzyme phycoerythrobilin synthase (PebS), recently discovered in a marine virus infecting oceanic cyanobacteria of the genus Prochlorococcus (cyanophage PSSM-2), is a new member of the ferredoxin-dependent bilin reductase (FDBR) family. In a formal four-electron reduction, the substrate biliverdin IXalpha is reduced to yield 3Z-PEB, a reaction that commonly requires the action of two individual FDBRs. The first reaction catalyzed by PebS is the reduction of the 15,16-methine bridge of the biliverdin IXalpha tetrapyrrole system. This reaction is exclusive to PEB biosynthetic enzymes. The second reduction site is the A-ring 2,3,3(1),3(2)-diene system, the most common target of FDBRs. Here, we present the first crystal structures of a PEB biosynthetic enzyme. Structures of the substrate complex were solved at 1.8- and 2.1-A resolution and of the substrate-free form at 1.55-A resolution. The overall folding revealed an alpha/beta/alpha-sandwich with similarity to the structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA). The substrate-binding site is located between the central beta-sheet and C-terminal alpha-helices. Eight refined molecules with bound substrate, from two different crystal forms, revealed a high flexibility of the substrate-binding pocket. The substrate was found to be either in a planar porphyrin-like conformation or in a helical conformation and is coordinated by a conserved aspartate/asparagine pair from the beta-sheet side. From the alpha-helix side, a conserved highly flexible aspartate/proline pair is involved in substrate binding and presumably catalysis.
 
  Selected figure(s)  
 
Figure 1.
FIGURE 1. Biosynthesis of PEB and PCB. PEB biosynthesis proceeds via two different pathways. PebA and PebB catalyze consecutive two-electron reductions of BV and 15,16-DHBV to yield PEB. PebS catalyzes the four-electron reduction of BV to PEB via the two-electron reduced intermediate 15,16-DHBV. PcyA catalyzes a four-electron reduction of biliverdin IX to PCB via the intermediate 18^1,18^2-DHBV. The electrons for all reactions come from reduced [2Fe-2S] ferredoxin (Fd[red]). The carbons of the respective reduction sites are numbered. Fd[ox], oxidized ferredoxin; P, propionate side chain.
Figure 3.
FIGURE 3. Stereoview of protein conformations observed in the crystal structures of PebS. Shown are C- traces of the superposed monomers of SePebS without substrate (gray), SePebS-BV with bound substrate (red; chains A–D), and wild-type PebS-BV with bound substrate (blue; chains A–D). Residue numbers are added in regular intervals.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 27547-27554) copyright 2008.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21050180 A.W.Busch, E.J.Reijerse, W.Lubitz, E.Hofmann, and N.Frankenberg-Dinkel (2011).
Radical mechanism of cyanophage phycoerythrobilin synthase (PebS).
  Biochem J, 433, 469-476.
PDB codes: 2x9i 2x9j
21250783 M.E.Auldridge, and K.T.Forest (2011).
Bacterial phytochromes: more than meets the light.
  Crit Rev Biochem Mol Biol, 46, 67-88.  
20491075 M.Kamio, L.Nguyen, S.Yaldiz, and C.D.Derby (2010).
How to produce a chemical defense: structural elucidation and anatomical distribution of aplysioviolin and phycoerythrobilin in the sea hare Aplysia californica.
  Chem Biodivers, 7, 1183-1197.  
19887371 Y.Hagiwara, M.Sugishima, H.Khawn, H.Kinoshita, K.Inomata, L.Shang, J.C.Lagarias, Y.Takahashi, and K.Fukuyama (2010).
Structural insights into vinyl reduction regiospecificity of phycocyanobilin:ferredoxin oxidoreductase (PcyA).
  J Biol Chem, 285, 1000-1007.
PDB codes: 3i8u 3i95
19159240 S.Stoll, A.Gunn, M.Brynda, W.Sughrue, A.C.Kohler, A.Ozarowski, A.J.Fisher, J.C.Lagarias, and R.D.Britt (2009).
Structure of the biliverdin radical intermediate in phycocyanobilin:ferredoxin oxidoreductase identified by high-field EPR and DFT.
  J Am Chem Soc, 131, 1986-1995.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.