2VCK

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

Summary for 2VCK

• Entry DOI: 10.2210/pdb2vck/pdb
• Related: 2VCL 2VGR
• Descriptor: CYANOBACTERIAL PHYCOERYTHROBILIN, BILIVERDINE IX ALPHA (3 entities in total)
• Functional Keywords: cyanophages, biliverdin ixa, oxidoreductase, phycobilin reductase, phycobilin synthesis, prochlorococcus, phycoerythrobilin, biliverdin reductase, ferredoxin dependent
• Biological source: PROCHLOROCOCCUS PHAGE P-SSM2
• Total number of polymer chains: 4
• Total formula weight: 112815.01

Authors

Dammeyer, T.,Hofmann, E.,Frankenberg-Dinkel, N. (deposition date: 2007-09-25, release date: 2008-08-05, Last modification date: 2024-10-16)

Primary citation

Dammeyer, T.,Hofmann, E.,Frankenberg-Dinkel, N.
Phycoerythrobilin Synthase (Pebs) of a Marine Virus: Crystal Structures of the Biliverdin Complex and the Substrate-Free Form.
J.Biol.Chem., 283:27547-, 2008

PubMed 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.

PubMed: 18662988
DOI: 10.1074/JBC.M803765200

Experimental method

X-RAY DIFFRACTION (1.8 Å)