title: COG3926 and COG5526: a tale of two new lysozyme-like protein families.
abstract: 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 phi8, 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.
authors.affiliation: Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390-9050, USA. jpei@chop.swmed.edu
authors.forename: Jimin
authors.initials: J
authors.lastname: Pei
authors.forename: Nick V
authors.initials: NV
authors.lastname: Grishin
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics; D002462:Cell Membrane / Q000737:chemistry / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D017910:Cystoviridae / Q000201:enzymology* / Q000235:genetics; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics; D009113:Muramidase / Q000737:chemistry* / Q000235:genetics; D017434:Protein Structure, Tertiary; D020539:Sequence Analysis, Protein / Q000379:methods; D014764:Viral Proteins / Q000737:chemistry*; D017355:Zymomonas / Q000201:enzymology* / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D014764:Viral Proteins; D009113:Muramidase