1QZQ

human Tyrosyl DNA phosphodiesterase

1QZQ の概要

• エントリーDOI: 10.2210/pdb1qzq/pdb
• 分子名称: tyrosyl-DNA phosphodiesterase 1 (2 entities in total)
• 機能のキーワード: dna repair, replication, hydrolase, dna binding protein
• 由来する生物種: Homo sapiens (human)
• 細胞内の位置: Nucleus : Q9NUW8
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 109838.68

構造登録者

Raymond, A.C.,Rideout, M.C.,Staker, B.,Hjerrild, K.,Burgin Jr., A.B. (登録日: 2003-09-17, 公開日: 2004-05-11, 最終更新日: 2024-02-14)

主引用文献

Raymond, A.C.,Rideout, M.C.,Staker, B.,Hjerrild, K.,Burgin Jr., A.B.
Analysis of Human Tyrosyl-DNA Phosphodiesterase I Catalytic Residues.
J.Mol.Biol., 338:895-906, 2004

PubMed Abstract: Tyrosyl-DNA phosphodiesterase I (Tdp1) is involved in the repair of DNA lesions created by topoisomerase I in vivo. Tdp1 is a member of the phospholipase D (PLD) superfamily of enzymes and hydrolyzes 3'-phosphotyrosyl bonds to generate 3'-phosphate DNA and free tyrosine in vitro. Here, we use synthetic 3'-(4-nitro)phenyl, 3'-(4-methyl)phenyl, and 3'-tyrosine phosphate oligonucleotides to study human Tdp1. Kinetic analysis of human Tdp1 (hTdp1) shows that the enzyme has nanomolar affinity for all three substrates and the overall in vitro reaction is diffusion-limited. Analysis of active-site mutants using these modified substrates demonstrates that hTdp1 uses an acid/base catalytic mechanism. The results show that histidine 493 serves as the general acid during the initial transesterification, in agreement with hypotheses based on previous crystal structure models. The results also argue that lysine 495 and asparagine 516 participate in the general acid reaction, and the analysis of crystal structures suggests that these residues may function in a proton relay. Together with previous crystal structure data, the new functional data provide a mechanistic understanding of the conserved histidine, lysine and asparagine residues found among all PLD family members.

PubMed: 15111055
DOI: 10.1016/j.jmb.2004.03.013

実験手法

X-RAY DIFFRACTION (2.4 Å)