Structural biology of DNA glycosylases
Grollman and Zharkov
Crystallographic analyses of DNA glycosylases bound to their cognate DNA substrates provide a rational basis for exploring the biochemical functions and substrate specificity of these proteins. Endo III and Ogg1 are members of the Endo III superfamily while Endo VIII and Fpg have the same novel fold. Ogg1 and Fpg share common structural motifs with Endo III and Endo VIII, respectively. By comparing the three dimensional structure of Fpg with Ogg1 and that of Endo III with Endo VIII—each complexed to its respective DNA substrate—we explore a central question in structural genomics, namely, how proteins with different tertiary structures perform identical biological functions. For DNA glycosylases, these include (a) binding to DNA and scanning the major groove for damage, ultimately forming a specific complex at the lesion site, (b) flipping the target base out of the DNA helix into a complementary pocket near the active site, and (c) nucleophilic attack at C1' accompanied by protonation of the heterocyclic ring to displace the damaged base.
- Kropachev K.Y., Zharkov D.O., Grollman A.P. Catalytic mechanism of Escherichia coli endonuclease VIII: Roles of the intercalation loop and the zinc finger. Biochemistry 45:12039-12049, 2006. PMID17002303
- Song K., Hornak V., de los Santo, C., Grollman A.P., Simmerling C. Computational analysis of the binding mode of 8-oxoguanine to formamidopyrimidine-DNA glycosylase. Biochemistry 45(36): 10886-94, 2006. PMID16953574
- Golan G., Zharkov D.O., Feinber, H., Fernandes, A.S., Zaika EI, Kycia J.H., Grollman A.P., Shoham G. Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. Nucleic Acids Res. 33: 5006-5016, 2005. PMID16145054
- Zharkov D.O., Grollman A.P. The DNA trackwalkers: principles of lesion search and recognition by DNA glycosylases. Mutation Research 33: 5006-16, 2005. PMID15939442
- Cheng X., Kelso C., Hornak V., de los Santos C., Grollman A.P., Simmerling C. Dynamic behavior of DNA base pairs containing 8-oxoguanine. J Am Chem Soc. 127: 13906-13918, 2005. PMID1620181