1Q3F

Uracil DNA glycosylase bound to a cationic 1-aza-2'-deoxyribose-containing DNA

Summary for 1Q3F

• Entry DOI: 10.2210/pdb1q3f/pdb
• Related: 1EMH 1SSP
• Descriptor: 5'-D(*TP*GP*TP*(NRI)P*AP*TP*CP*TP*T)-3', 5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3', Uracil-DNA glycosylase, ... (6 entities in total)
• Functional Keywords: udg, dna repair, hydrolase-dna complex, hydrolase/dna
• Biological source: Homo sapiens (human)
• Cellular location: Isoform 1: Mitochondrion. Isoform 2: Nucleus: P13051
• Total number of polymer chains: 3
• Total formula weight: 31407.98

Authors

Bianchet, M.A.,Seiple, L.A.,Jiang, Y.L.,Ichikawa, Y.,Amzel, L.M.,Stivers, J.T. (deposition date: 2003-07-29, release date: 2004-03-23, Last modification date: 2023-08-16)

Primary citation

Bianchet, M.A.,Seiple, L.A.,Jiang, Y.L.,Ichikawa, Y.,Amzel, L.M.,Stivers, J.T.
Electrostatic guidance of glycosyl cation migration along the reaction coordinate of uracil DNA glycosylase.
Biochemistry, 42:12455-12460, 2003

PubMed Abstract: The DNA repair enzyme uracil DNA glycosylase has been crystallized with a cationic 1-aza-2'-deoxyribose-containing DNA that mimics the ultimate transition state of the reaction in which the water nucleophile attacks the anomeric center of the oxacarbenium ion-uracil anion reaction intermediate. Comparison with substrate and product structures, and the previous structure of the intermediate determined by kinetic isotope effects, reveals an exquisite example of geometric strain, least atomic motion, and electrophile migration in biological catalysis. This structure provides a rare opportunity to reconstruct the detailed structural transformations that occur along an enzymatic reaction coordinate.

PubMed: 14580190
DOI: 10.1021/bi035372+

Experimental method

X-RAY DIFFRACTION (1.9 Å)