1EMH

CRYSTAL STRUCTURE OF HUMAN URACIL-DNA GLYCOSYLASE BOUND TO UNCLEAVED SUBSTRATE-CONTAINING DNA

1EMH の概要

• エントリーDOI: 10.2210/pdb1emh/pdb
• 関連するPDBエントリー: 1AKZ 1SSP 2SSP 4SKN
• 分子名称: DNA (5'-D(*TP*GP*TP*(P2U)P*AP*TP*CP*TP*T)-3'), DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3'), URACIL-DNA GLYCOSYLASE, ... (4 entities in total)
• 機能のキーワード: alpha/beta fold, uracil-dna glycosylase, protein/dna, hydrolase-dna complex, hydrolase/dna
• 由来する生物種: Homo sapiens (human)
• 細胞内の位置: Isoform 1: Mitochondrion. Isoform 2: Nucleus: P13051
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 31311.98

構造登録者

Parikh, S.S.,Slupphaug, G.,Krokan, H.E.,Blackburn, G.M.,Tainer, J.A. (登録日: 2000-03-16, 公開日: 2000-05-16, 最終更新日: 2024-02-07)

主引用文献

Parikh, S.S.,Walcher, G.,Jones, G.D.,Slupphaug, G.,Krokan, H.E.,Blackburn, G.M.,Tainer, J.A.
Uracil-DNA glycosylase-DNA substrate and product structures: conformational strain promotes catalytic efficiency by coupled stereoelectronic effects.
Proc.Natl.Acad.Sci.USA, 97:5083-5088, 2000

PubMed Abstract: Enzymatic transformations of macromolecular substrates such as DNA repair enzyme/DNA transformations are commonly interpreted primarily by active-site functional-group chemistry that ignores their extensive interfaces. Yet human uracil-DNA glycosylase (UDG), an archetypical enzyme that initiates DNA base-excision repair, efficiently excises the damaged base uracil resulting from cytosine deamination even when active-site functional groups are deleted by mutagenesis. The 1.8-A resolution substrate analogue and 2.0-A resolution cleaved product cocrystal structures of UDG bound to double-stranded DNA suggest enzyme-DNA substrate-binding energy from the macromolecular interface is funneled into catalytic power at the active site. The architecturally stabilized closing of UDG enforces distortions of the uracil and deoxyribose in the flipped-out nucleotide substrate that are relieved by glycosylic bond cleavage in the product complex. This experimentally defined substrate stereochemistry implies the enzyme alters the orientation of three orthogonal electron orbitals to favor electron transpositions for glycosylic bond cleavage. By revealing the coupling of this anomeric effect to a delocalization of the glycosylic bond electrons into the uracil aromatic system, this structurally implicated mechanism resolves apparent paradoxes concerning the transpositions of electrons among orthogonal orbitals and the retention of catalytic efficiency despite mutational removal of active-site functional groups. These UDG/DNA structures and their implied dissociative excision chemistry suggest biology favors a chemistry for base-excision repair initiation that optimizes pathway coordination by product binding to avoid the release of cytotoxic and mutagenic intermediates. Similar excision chemistry may apply to other biological reaction pathways requiring the coordination of complex multistep chemical transformations.

PubMed: 10805771
DOI: 10.1073/pnas.97.10.5083

実験手法

X-RAY DIFFRACTION (1.8 Å)