Crystal structure ofEscherichia coli uracil DNA glycosylase and its complexes with uracil and glycerol: Structure and glycosylase mechanism revisited

Autor: Jaya Jagadeesh, Gary L. Gilliland, Alexander C. Drohat, Gaoyi Xiao, James T. Stivers, Maria Tordova
Rok vydání: 1999
Předmět:
Zdroj: Proteins: Structure, Function, and Genetics. 35:13-24
ISSN: 1097-0134
0887-3585
DOI: 10.1002/(sici)1097-0134(19990401)35:1<13::aid-prot2>3.0.co;2-2
Popis: The DNA repair enzyme uracil DNA glycosylase (UDG) catalyzes the hydrolysis of premu- tagenic uracil residues from single-stranded or du- plex DNA, producing free uracil and abasic DNA. Here we report the high-resolution crystal struc- tures of free UDG from Escherichia coli strain B (1.60 A ˚ ), its complex with uracil (1.50 A ˚ ), and a second active-site complex with glycerol (1.43 A ˚ ). These represent the first high-resolution structures of a prokaryotic UDG to be reported. The overall structure of the E. coli enzyme is more similar to the human UDG than the herpes virus enzyme. Signifi- cant differences between the bacterial and viral structures are seen in the side-chain positions of the putative general-acid (His187) and base (Asp64), similar to differences previously observed between the viral and human enzymes. In general, the active- site loop that contains His187 appears preorganized in comparison with the viral and human enzymes, requiring smaller substrate-induced conformational changes to bring active-site groups into catalytic position. These structural differences may be re- lated to the large differences in the mechanism of uracil recognition used by the E. coli and viral enzymes. The pH dependence of kcat for wild-type UDG and the D64N and H187Q mutant enzymes is consistent with general-base catalysis by Asp64, but provides no evidence for a general-acid catalyst. The catalytic mechanism of UDG is critically dis- cussed with respect to these results. Proteins
Databáze: OpenAIRE
Externí odkaz: