PMID:15273316

Citation	Cheng, H, Shen, N, Pei, J and Grishin, NV (2004) Double-stranded DNA bacteriophage prohead protease is homologous to herpesvirus protease. Protein Sci. 13:2260-9
Abstract	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.
Links	PubMed PMC2279824 Online version:10.1110/ps.04726004
Keywords	Amino Acid Sequence; Bacteriophages/enzymology; DNA; Endopeptidases/chemistry; Endopeptidases/classification; Herpesviridae/enzymology; Molecular Sequence Data; Protein Folding; Protein Structure, Tertiary; Sequence Alignment; Sequence Homology, Amino Acid; Viral Core Proteins/chemistry; Viral Core Proteins/classification; Viral Proteins/chemistry; Viral Proteins/classification
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Significance

This paper shows that two families of viral prohead maturation proteases can be unified into a larger superfamily.

Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
BPT4:D9IEK7		GO:0006508: proteolysis	ECO:0000250:		P		From the fourth paragraph under results,"in the course of expanding the U35.001 family, we found statistical evidence that the U9 family and the U35.001 family are remote homologs. For example, starting with the U35.001 representative HK97 gp4 protease (gi|9634157, residues 1–225), PSI-BLAST search found a close homolog gi|26988298 with e-value 2e-18 in the first iteration. Using this sequence as query to run PSI-BLAST (default parameters in NCBI Web site), we found a U9 family member (gi|30044105) in the third iteration with a significant e-value 0.003."	Missing: with/from CACAO 11664
BPT4:D9IEK7		GO:0006508: proteolysis	ECO:0000247:		P		Figure 2A Euclidian distance map. "In distance mapping, each sequence is represented by a point in a multidimensional Euclidian space and the distances between these points reflect the evolutionary distances between the sequences. A two-dimensional projection of this space is shown in Figure 2A ▶ (below). This plot offers a visualization of the sequence clustering; each family or subfamily appears as a rather distinct group, except for U35.002.a and U35.002.c. These two subfamilies are divided on the basis of sequence conservation and insertion/ deletion patterns."	Missing: with/from CACAO 11670

References

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