Phycoerythrobilin synthase (PebS) of a marine virus. Crystal structures of the biliverdin complex and the substrate-free form.
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.
Dammeyer
Thorben
T
Physiology of Microorganisms, Ruhr-Universität Bochum, D-44780 Bochum, Germany.
Hofmann
Eckhard
E
Biophysics, Department of Biology and Biotechnology, Ruhr-Universität Bochum, D-44780 Bochum, Germany. Electronic address: eckhard.hofmann@bph.rub.de.
Frankenberg-Dinkel
Nicole
N
Physiology of Microorganisms, Ruhr-Universität Bochum, D-44780 Bochum, Germany. Electronic address: nicole.frankenberg@rub.de.
D001435:Bacteriophages / Q000201:enzymology*; D001665:Binding Sites; D002384:Catalysis; D018360:Crystallography, X-Ray; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000737:chemistry* / Q000378:metabolism; D052980:Phycobilins / Q000096:biosynthesis; D010799:Phycoerythrin / Q000096:biosynthesis; D048929:Prochlorococcus / Q000201:enzymology / Q000821:virology*; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040681:Structural Homology, Protein; D014764:Viral Proteins / Q000737:chemistry* / Q000378:metabolism
D052980:Phycobilins; D014764:Viral Proteins; D010799:Phycoerythrin; C011070:phycoerythrobilin; D010088:Oxidoreductases