5U7X

Crystal structure of a nucleoside triphosphate diphosphohydrolase (NTPDase) from the legume Vigna unguiculata subsp. cylindrica (Dolichos biflorus) in complex with phosphate and manganese

5U7X の概要

• エントリーDOI: 10.2210/pdb5u7x/pdb
• 関連するPDBエントリー: 5U7P 5U7V 5U7W
• 分子名称: Nod factor binding lectin-nucleotide phosphohydrolase, PHOSPHATE ION, MANGANESE (II) ION, ... (4 entities in total)
• 機能のキーワード: apyrase, ntpdase, rnase-h fold, mixed 5 strand beta-sheet, hydrolase
• 由来する生物種: Vigna unguiculata subsp. cylindrica (Horse gram)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 48409.16

構造登録者

Cumming, M.H.,Summers, E.L.,Oulavallickal, T.,Roberts, N.,Arcus, V.L. (登録日: 2016-12-12, 公開日: 2017-05-31, 最終更新日: 2024-11-06)

主引用文献

Summers, E.L.,Cumming, M.H.,Oulavallickal, T.,Roberts, N.J.,Arcus, V.L.
Structures and kinetics for plant nucleoside triphosphate diphosphohydrolases support a domain motion catalytic mechanism.
Protein Sci., 26:1627-1638, 2017

PubMed Abstract: Extracellular nucleoside triphosphate diphosphohydrolases (NTPDases) are enzymes that hydrolyze extracellular nucleotides to the respective monophosphate nucleotides. In the past 20 years, NTPDases belonging to mammalian, parasitic and prokaryotic domains of life have been discovered, cloned and characterized. We reveal the first structures of NTPDases from the legume plant species Trifolium repens (7WC) and Vigna unguiculata subsp. cylindrica (DbLNP). Four crystal structures of 7WC and DbLNP were determined at resolutions between 1.9 and 2.6 Å. For 7WC, structures were determined for an -apo form (1.89 Å) and with the product AMP (2.15 Å) and adenine and phosphate (1.76 Å) bound. For DbLNP, a structure was solved with phosphate and manganese bound (2.60 Å). Thorough kinetic data and analysis is presented. The structure of 7WC and DbLNP reveals that these NTPDases can adopt two conformations depending on the molecule and co-factor bound in the active site. A central hinge region creates a "butterfly-like" motion of the domains that reduces the width of the inter-domain active site cleft upon molecule binding. This phenomenon has been previously described in Rattus norvegicus and Legionella pneumophila NTPDaseI and Toxoplasma gondii NTPDaseIII suggesting a common catalytic mechanism across the domains of life.

PubMed: 28543850
DOI: 10.1002/pro.3199

実験手法

X-RAY DIFFRACTION (2.6 Å)