ANALYSIS OF A PCNA-BINDING SITE IN DIVERSE PROTEIN FAMILIES

Analysis of a PCNA-Binding Site in Diverse Protein Families

Marcus, S. and Pietrokovski, S.
Department of Molecular Genetics, Weizmann Institute of Science

Proliferating Cell Nuclear Antigen (PCNA) is a major factor in DNA replication, DNA repair and cell cycle control mechanisms. It is found in two of the three major domains of life: Archaea and Eukarya. PCNA is an accessory for DNA-processive proteins, such as DNA polymerases, DNA-repair proteins etc. Several PCNA-binding proteins were shown to bind PCNA in a competitive manner, suggesting a common binding site for these proteins on PCNA, hence a common PCNA-binding motif in these proteins. One of these PCNA-binding proteins is the cell-cycle control protein p21^Cip1. A synthetic peptide derived from human p21^Cip1 was co-crystallized with PCNA. This offered an insight to the interaction between PCNA and the proteins that bind to it. The sequence motif of the PCNA-binding site that is shared among p21^Cip1 and other proteins was termed: p21-like PCNA-binding site. A sequence pattern for this motif was offered: Q-x-x-h-x-x-a-a, where 'x' is any amino acid, 'h' is a hydrophobic residue and 'a' is an aromatic residue. This sequence pattern is used for searching for new PCNA-binding proteins. However, a search with this pattern gives a large number of unranked hits that includes many false hits. Thus, identifying true hits is very difficult. Multiple sequence alignments are well documented to be superior to pattern and single-sequence queries in database searches.

We present here a block alignment based method for identifying PCNA-binding proteins. The method has better sensitivity (identifying true hits) and selectivity (avoiding false hits) then pattern and sequence searches. We identified new PCNA-binding sites in several families, including some not even known to bind. Some of the sites appear in a different sequence context then known PCNA-binding sites. Our analysis also allows us to study the convergent evolution of these sites and the effect of various selection pressures on them.