1SM8

M. tuberculosis dUTPase complexed with chromium and dUTP

1SM8 の概要

• エントリーDOI: 10.2210/pdb1sm8/pdb
• 関連するPDBエントリー: 1MQ7 1SIX 1SJN 1SLH 1SMC
• 分子名称: Deoxyuridine 5'-triphosphate nucleotidohydrolase, CHROMIUM ION, NITRATE ION, ... (6 entities in total)
• 機能のキーワード: jelly-roll, structural genomics, psi, protein structure initiative, tb structural genomics consortium, tbsgc, hydrolase
• 由来する生物種: Mycobacterium tuberculosis
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 55721.50

構造登録者

Sawaya, M.R.,Chan, S.,Segelke, B.,Lekin, T.,Krupka, H.,Cho, U.S.,Kim, M.-Y.,So, M.,Kim, C.-Y.,Naranjo, C.M.,Rogers, Y.C.,Park, M.S.,Waldo, G.S.,Pashkov, I.,Cascio, D.,Yeates, T.O.,Perry, J.L.,Terwilliger, T.C.,Eisenberg, D.,TB Structural Genomics Consortium (TBSGC) (登録日: 2004-03-08, 公開日: 2004-03-16, 最終更新日: 2023-08-23)

主引用文献

Chan, S.,Segelke, B.,Lekin, T.,Krupka, H.,Cho, U.S.,Kim, M.-Y.,So, M.,Kim, C.-Y.,Naranjo, C.M.,Rogers, Y.C.,Park, M.S.,Waldo, G.S.,Pashkov, I.,Cascio, D.,Perry, J.L.,Sawaya, M.R.
Crystal structure of the Mycobacterium tuberculosis dUTPase: insights into the catalytic mechanism.
J.Mol.Biol., 341:503-517, 2004

PubMed Abstract: The structure of Mycobacterium tuberculosis dUTP nucleotidohydrolase (dUTPase) has been determined at 1.3 Angstrom resolution in complex with magnesium ion and the non-hydrolyzable substrate analog, alpha,beta-imido dUTP. dUTPase is an enzyme essential for depleting potentially toxic concentrations of dUTP in the cell. Given the importance of its biological role, it has been proposed that inhibiting M.tuberculosis dUTPase might be an effective means to treat tuberculosis infection in humans. The crystal structure presented here offers some insight into the potential for designing a specific inhibitor of the M.tuberculosis dUTPase enzyme. The structure also offers new insights into the mechanism of dUTP hydrolysis by providing an accurate representation of the enzyme-substrate complex in which both the metal ion and dUTP analog are included. The structure suggests that inclusion of a magnesium ion is important for stabilizing the position of the alpha-phosphorus for an in-line nucleophilic attack. In the absence of magnesium, the alpha-phosphate of dUTP can have either of the two positions which differ by 4.5 Angstrom. A transiently ordered C-terminal loop further assists catalysis by shielding the general base, Asp83, from solvent thus elevating its pK(a) so that it might in turn activate a tightly bound water molecule for nucleophilic attack. The metal ion coordinates alpha, beta, and gamma phosphate groups with tridentate geometry identical with that observed in the crystal structure of DNA polymerase beta complexed with magnesium and dNTP analog, revealing some common features in catalytic mechanism.

PubMed: 15276840
DOI: 10.1016/j.jmb.2004.06.028

実験手法

X-RAY DIFFRACTION (2.9 Å)