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FOR THE RECORD

The P5 protein from bacteriophage phi-6 is a distant homolog of lytic transglycosylases

¹ Department of Biochemistry and ² Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, USA

(RECEIVED November 19, 2004; FINAL REVISION January 19, 2005; ACCEPTED January 20, 2005)

Peptidases are classical objects of enzymology and structural studies. However, a few protein families with experimentally characterized proteolytic activity, but unknown catalytic mechanism and three-dimensional structures, still exist. Using comparative sequence analysis, we deduce spatial structure for one of such families, namely, U40, which contains just one P5 protein from bacteriophage phi-6. We show that this singleton sequence possesses conserved sequence motifs characteristic of lysozymes and is a distant homolog of lytic transglycosylases that cleave bacterial peptidoglycan. The structure of the P5 protein is therefore predicted to adopt the lysozyme-like fold shared by T4, , C-type, G-type lysozymes, and lytic transglycosylases. Since previous biochemical experiments with P5 of phi-6 have indicated that the purified enzyme possesses endopeptidase activity and not glycosidase activity, our results point to the possibility of a newly evolved molecular function and call for further experimental characterization of this unusual P5 protein.

Keywords: structure prediction; bacteriophage phi-6; peptidase; lytic transglycosylase; lysozyme; comparative phage genomics

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041250005.

Reprint requests to: Jimin Pei, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA; e-mail: jpei{at}chop.swmed.edu; fax: (214) 648-9099.

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