PDBsum entry 2vcl

Oxidoreductase

PDB id: 2vcl

Contents

Protein chain

205 a.a. *

Ligands

GOL ×3

Waters ×225

* Residue conservation analysis

PDB id:

2vcl

Name:

Oxidoreductase

Title:

Structure of phycoerythrobilin synthase pebs from the cyanophage p- ssm2 in the substrate free form

Structure:

Cyanobacterial phycoerythrobilin. Chain: a. 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:

1.55Å R-factor: 0.174 R-free: 0.194

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

Protein chain

Q58MU6  (PEBS_BPPRM) -  Phycoerythrobilin synthase from Prochlorococcus phage P-SSM2

Seq: 233 a.a.

Struc: 205 a.a.

Enzyme reactions

• Enzyme class: E.C.1.3.7.6 - phycoerythrobilin synthase.
• Reaction: (3Z)-phycoerythrobilin + 2 oxidized 2[4Fe-4S]-[ferredoxin] = biliverdin IXalpha + 2 reduced 2[4Fe-4S]-[ferredoxin] + 4 H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Key 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.