Prediction-based threading of the hMSH2 DNA mismatch repair protein

^a Department of Medicine and the Cancer Center, University of California, San Diego, La Jolla, California 92093–0058, USA
^b San Diego Super Computer Center, La Jolla, California 92093, USA

Mutations in the genes whose products participate in DNA mismatch repair underlie the increased risk of cancer in families with hereditary nonpolyposis colon carcinoma. Mutations in hMSH2 account for approximately 50% of the mutations found in these families. We sought to predict the 3-dimensional structure of hMSH2 by identifying structural homologues using prediction-based threading and by computer modeling using information from these putative structurally related proteins. Prediction-based threading identified three candidate structural homologues: glycogen phosphorylase (gpb), a 70 kDa soluble lytic transglycosylase, and ribonucleotide reductase protein R1. An independent approach utilizing a potential-based threading program also identified gpb as a structural homologue. The models based on the structures of these proteins suggest that the ATP binding domain and helix-turn-helix domain are exposed on the outside of the protein. All known bacterial MutS and hMSH2 mutations appear to be clustered in similar vicinities in the theoretical models of hMSH2; the major site is within the ATP binding domain and near the carboxyl-terminal end, whereas a smaller number map to the region coding for exon 5 and the amino-terminal domain. All point mutations also appear to affect amino acids that are exposed on the outside surface of the protein.—de las Alas, M. M., de Bruin, R. A. M., Ten Eyck, L., Los, G., Howell, S. B. Prediction-based threading of the hMSH2 DNA mismatch repair protein. FASEB J. 12, 653–663 (1998)

Key Words: protein model • loop generation • structural homoloque • glycogen phosphorylase

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