Phycoerythrobilin Synthase (PebS) of a Marine Virus: CRYSTAL STRUCTURES OF THE BILIVERDIN COMPLEX AND THE SUBSTRATE-FREE FORM

• Published in: The Journal of biological chemistry 2008-10, Vol.283 (41), p.27547-27554
• Main Authors: Dammeyer, Thorben, Hofmann, Eckhard, Frankenberg-Dinkel, Nicole
• Format: Article
• Language: English
• Subjects: Bacteriophages - enzymology; Binding Sites; Catalysis; Crystallography, X-Ray; Oxidation-Reduction; Oxidoreductases - chemistry; Oxidoreductases - metabolism; Phycobilins - biosynthesis; Phycoerythrin - biosynthesis; Prochlorococcus - enzymology; Prochlorococcus - virology; Protein Structure, Secondary; Protein Structure, Tertiary; Structural Homology, Protein; Viral Proteins - chemistry; Viral Proteins - metabolism
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M803765200

The reddish purple open chain tetrapyrrole pigment phycoerythrobilin (PEB; Aλmax ~ 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 IXα 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 IXα tetrapyrrole system. This reaction is exclusive to PEB biosynthetic enzymes. The second reduction site is the A-ring 2,3,3¹,3²-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-Å resolution and of the substrate-free form at 1.55-Å resolution. The overall folding revealed an α/β/α-sandwich with similarity to the structure of phycocyanobilin:ferredoxin oxidoreductase (PcyA). The substrate-binding site is located between the central β-sheet and C-terminal α-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 β-sheet side. From the α-helix side, a conserved highly flexible aspartate/proline pair is involved in substrate binding and presumably catalysis.