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FOR THE RECORD

Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease

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

(RECEIVED March 8, 2004; FINAL REVISION May 10, 2004; ACCEPTED May 14, 2004)

Double-stranded DNA bacteriophages and herpesviruses assemble their heads in a similar fashion; a pre-formed precursor called a prohead or procapsid undergoes a conformational transition to give rise to a mature head or capsid. A virus-encoded prohead or procapsid protease is often required in this maturation process. Through computational analysis, we infer homology between bacteriophage prohead proteases (MEROPS families U9 and U35) and herpesvirus protease (MEROPS family S21), and unify them into a procapsid protease superfamily. We also extend this superfamily to include an uncharacterized cluster of orthologs (COG3566) and many other phage or bacteria-encoded hypothetical proteins. On the basis of this homology and the herpesvirus protease structure and catalytic mechanism, we predict that bacteriophage prohead proteases adopt the herpesvirus protease fold and exploit a conserved Ser and His residue pair in catalysis. Our study provides further support for the proposed evolutionary link between dsDNA bacteriophages and herpesviruses.

Keywords: dsDNA bacteriophage; prohead protease; MEROPS; homology detection; structure prediction; gene organization; evolution

Abbreviations: PDB, Protein Data Bank • PSI-BLAST, position-specific iterated basic local alignment search tool • COG, clusters of orthologous groups • 3D, three-dimensional • dsDNA, double-stranded DNA • PCMA, profile consistency multiple sequence alignment.

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

Supplemental material: see ftp://iole.swmed.edu/pub/cheng/prohead

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.04726004.

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