 |
PDBsum entry 2vcl
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Oxidoreductase
|
PDB id
|
|
|
|
2vcl
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Phycoerythrobilin synthase (pebs) of a marine virus: crystal structures of the biliverdin complex and the substrate-Free form.
|
|
|
Authors
|
|
T.Dammeyer,
E.Hofmann,
N.Frankenberg-Dinkel.
|
|
|
Ref.
|
|
J Biol Chem, 2008,
283,
27547-27554.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
|
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.
|
|
|
|
|
|
|
