Positively Charged Residues within the Iron–Sulfur Cluster Loop of E. coli MutY Participate in Damage Recognition and Removal

Abstract

Escherichia coli MutY is an adenine glycosylase involved in base excision repair that recognizes OG:A (where OG = 7,8-dihydro-8-oxo-2′-deoxyguanosine) and G:A mismatches in DNA. MutY contains a solvent-exposed polypeptide loop between two of the cysteine ligands to the [4Fe–4S]2+ cluster, referred to as the iron–sulfur cluster loop (FCL) motif. The FCL is located adjacent to the proposed active site pocket and has been suggested to be part of the DNA binding surface of MutY (Y. Guan et al., 1998, Nat. Struct. Biol. 5, 1058–1064). In order to investigate the role of specific residues within the FCL motif, we have determined the effects of replacing arginine 194, lysine 196, and lysine 198 with alanine on the enzymatic properties of MutY. The properties of the R194A, K196A, and K198A enzymes were also compared to the properties of mutated enzymes in which lysine residues near the active site pocket were replaced with alanine or glycine. Substrate recognition was evaluated using a duplex containing a 2′-deoxyadenosine analog in a base pair opposite G or OG. These results indicate that removal of positively charged amino acids within the FCL and the active site compromise the ability of the enzyme to bind to the substrate analog. However, only the K198A enzyme exhibited a significant reduction (15-fold) of the rate of adenine removal from a G:A base pair-containing duplex. This is the first direct evidence that Lys 198 within the FCL motif of MutY has a role in specific damage recognition and removal. Furthermore, these results suggest that the FCL motif is intimately involved in the base removal process.