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J. Biol. Chem., Vol. 283, Issue 41, 27547-27554, October 10, 2008

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Phycoerythrobilin Synthase (PebS) of a Marine Virus

CRYSTAL STRUCTURES OF THE BILIVERDIN COMPLEX AND THE SUBSTRATE-FREE FORM^*

Thorben Dammeyer¹, Eckhard Hofmann², and Nicole Frankenberg-Dinkel³

From the Physiology of Microorganisms, and Biophysics, Department of Biology and Biotechnology, Ruhr-Universität Bochum, D-44780 Bochum, Germany

The reddish purple open chain tetrapyrrole pigment phycoerythrobilin (PEB; A_max 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 IX 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 IX 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 /β/-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 -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 -helix side, a conserved highly flexible aspartate/proline pair is involved in substrate binding and presumably catalysis.

Received for publication, May 16, 2008 , and in revised form, July 7, 2008.

^* This work was supported by Sonderforschungsbereich 480 from the Deutsche Forschungsgemeinschaft (Teilprojekt C6 and C8; to E. H. and N. F.-D.). The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

The on-line version of this article (available at http://www.jbc.org) contains supplemental Figs. S1–S8 and Tables S1 and S2. The atomic coordinates and structure factors (codes 2VCL, 2VCK, and 2VGR) have been deposited in the Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers University, New Brunswick, NJ (http://www.rcsb.org/).

This article was selected as a Paper of the Week.

¹ Present address: Environmental Microbiology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, D-38124 Braunschweig, Germany.

² To whom correspondence may be addressed: Protein Crystallography, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany. Fax: 49-234-321-4626; E-mail: eckhard.hofmann{at}bph.rub.de. ³To whom correspondence may be addressed: Physiology of Microorganisms, Ruhr-Universität Bochum, Universitätsstr. 150, D-44780 Bochum, Germany. Fax: 49-234-321-4620; E-mail: nicole.frankenberg{at}rub.de.

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