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Published online before print September 9, 2005
Protein Science, DOI: 10.1110/ps.051656805
 Copyright © 2005 The Protein Society
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COG3926 and COG5526: A tale of two new lysozyme-like protein families

Jimin Pei1 and Nick V. Grishin1,2

1 Department of Biochemistry and 2 Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050, USA

(RECEIVED June 20, 2005; FINAL REVISION July 18, 2005; ACCEPTED July 22, 2005)

We have identified two new lysozyme-like protein families by using a combination of sequence similarity searches, domain architecture analysis, and structural predictions. First, the P5 protein from bacteriophage {phi}8, which belongs to COG3926 and Pfam family DUF847, is predicted to have a new lysozyme-like domain. This assignment is consistent with the lytic function of P5 proteins observed in several related double-stranded RNA bacteriophages. Domain architecture analysis reveals two lysozyme-associated transmembrane modules (LATM1 and LATM2) in a few COG3926/DUF847 members. LATM2 is also present in two proteins containing a peptidoglycan binding domain (PGB) and an N-terminal region that corresponds to COG5526 with uncharacterized function. Second, structure prediction and sequence analysis suggest that COG5526 represents another new lysozyme-like family. Our analysis offers fold and active-site assignments for COG3926/DUF847 and COG5526. The predicted enzymatic activity is consistent with an experimental study on the zliS gene product from Zymomonas mobilis, suggesting that bacterial COG3926/DUF847 members might be activators of macromolecular secretion.

Keywords: lysozyme; structure prediction; bacteriophage {phi}8; lysozyme-associated transmembrane modules; macromolecular secretion

Article published online ahead of print. Article and publication date are at http://www.proteinscience.org/cgi/doi/10.1110/ps.051656805.

Reprint requests to: Jimin Pei, Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9050, USA; e-mail: jpei{at}chop.swmed.edu; fax: (214) 645-5948.

Supplemental material: see www.proteinscience.org


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