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6AJO

Complex form of Uracil DNA glycosylase X and uracil-DNA.

Summary for 6AJO
Entry DOI10.2210/pdb6ajo/pdb
DescriptorUracil DNA glycosylase superfamily protein, DNA (5'-D(P*(ORP)P*TP*T)-3'), IRON/SULFUR CLUSTER, ... (6 entities in total)
Functional Keywordsdna repair, base excision, dna-protein crosslink., dna binding protein
Biological sourceMycobacterium smegmatis MC2 155
More
Total number of polymer chains2
Total formula weight24127.89
Authors
Ahn, W.C.,Aroli, S.,Varshney, U.,Woo, E.J. (deposition date: 2018-08-28, release date: 2019-05-29, Last modification date: 2024-03-27)
Primary citationAhn, W.C.,Aroli, S.,Kim, J.H.,Moon, J.H.,Lee, G.S.,Lee, M.H.,Sang, P.B.,Oh, B.H.,Varshney, U.,Woo, E.J.
Covalent binding of uracil DNA glycosylase UdgX to abasic DNA upon uracil excision.
Nat.Chem.Biol., 15:607-614, 2019
Cited by
PubMed Abstract: Uracil DNA glycosylases (UDGs) are important DNA repair enzymes that excise uracil from DNA, yielding an abasic site. Recently, UdgX, an unconventional UDG with extremely tight binding to DNA containing uracil, was discovered. The structure of UdgX from Mycobacterium smegmatis in complex with DNA shows an overall similarity to that of family 4 UDGs except for a protruding loop at the entrance of the uracil-binding pocket. Surprisingly, H109 in the loop was found to make a covalent bond to the abasic site to form a stable intermediate, while the excised uracil remained in the pocket of the active site. H109 functions as a nucleophile to attack the oxocarbenium ion, substituting for the catalytic water molecule found in other UDGs. To our knowledge, this change from a catalytic water attack to a direct nucleophilic attack by the histidine residue is unprecedented. UdgX utilizes a unique mechanism of protecting cytotoxic abasic sites from exposure to the cellular environment.
PubMed: 31101917
DOI: 10.1038/s41589-019-0289-3
PDB entries with the same primary citation
Experimental method
X-RAY DIFFRACTION (2.269 Å)
Structure validation

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