Domain closure and action of uracil DNA glycosylase (UDG): structures of new crystal forms containing the Escherichia coli enzyme and a comparative study of the known structures involving UDG

Abstract

The structures of a new crystal form of free Escherichia coli uracil DNA glycosylase (UDG), containing four molecules in the asymmetric unit, and two forms of its complex with the proteinaceous inhibitor Ugi, containing two and four crystallographically independent complexes, have been determined. A comparison of these structures and the already known crystal structures containing UDG shows that the enzyme can be considered to be made up of two independently moving structural entities or domains. A detailed study of free and DNA‐bound human enzyme strengthens this conclusion. The domains close upon binding to uracil‐containing DNA, whereas they do not appear to do so upon binding to Ugi. The comparative study also shows that the mobility of the molecule involves the rigid‐body movement of the domains superposed on flexibility within domains.

A Decade of Biochemical and Structural Studies of the DNA Repair Machinery of Deinococcus radiodurans: Major Findings, Functional and Mechanistic Insight and Challenges

“…They remove uracil, formed as a result of deamination of cytosine [33] or mis-incorporated during replication [34], from DNA. The drUNG structure was determined to a resolution of 1.8 Å [28] and showed high similarity to previously determined structures of human [35], herpes simplex virus [36], E. coli [37] and Atlantic cod [38] UNGs. However, drUNG was shown to possess a very high catalytic efficiency on uracil containing substrate (mainly U:A and U:G base pairs) compared to human UNG, which was attributed to a high substrate affinity caused by a cluster of positively charged residues close to the DNA binding site [28].…”

Uracil-DNA glycosylase: Structural, thermodynamic and kinetic aspects of lesion search and recognition

“…At the moment of writing this review, the Protein Data Bank held 43 structures of UNG enzymes from human [21,23–30], Atlantic cod [31,32], Leischmania naiffi (Larson et al, to be published), E. coli [33–38], Mycobacterium tuberculosis [39], Deinococcus radiodurans [40], Vibrio cholerae (Raeder et al, to be published), herpes simplex virus 1 [22,41,42], Epstein–Barr virus [43] and vaccinia virus [44], either free or complexed with Ura, dUrd, various ss- and ds oligodeoxyribonucleotides (ODNs), and inhibitors, both naturally occurring (Ugi protein of PBS bacteriophages) and designed small molecules. Since the general structures of all these proteins and features of their interaction with DNA are quite similar, it makes sense to consider all UNG proteins as minor variations of a single structural system.…”

Crystal structure and functional insights into uracil-DNA glycosylase inhibition by phage ϕ29 DNA mimic protein p56

“…Previous studies have determined that the mechanism for uracil repairing by UDGs in diverse organisms included the displacement of the uracil lesion to an extrahelical position and the insertion into the DNA base stack of the side chain of a protruding leucine (Leu272 in Hs UDG, Leu191 in Ec UDG) located at UDG loop V (14,38,45). Interestingly, our analysis revealed that the main feature of the Bs UDG-p56 complex formation is the recognition of the Phe191 residue from Bs UDG by a specific hydrophobic pocket at the p56 dimer interface (Figure 7B).…”

“…Therefore, to model the Bs UDG-DNA complex, Bs UDG coordinates were separated in two domains [domain I (8–79; 120–154) and domain II (80–111; 159–225], as their equivalent domains in several UDG isoforms are reported to close on DNA binding (38). Each domain was superposed to Hs UDG (50% sequence identity), as obtained in complex with DNA (pdb code 1emh).…”