3RRP

Crystal structure of fumarate hydratase Fum from Mycobacterium abscessus with malate bound

3RRP の概要

• エントリーDOI: 10.2210/pdb3rrp/pdb
• 関連するPDBエントリー: 3RD8
• 分子名称: Probable fumarate hydratase Fum, (2S)-2-hydroxybutanedioic acid, 1,2-ETHANEDIOL, ... (4 entities in total)
• 機能のキーワード: structural genomics, seattle structural genomics center for infectious disease, ssgcid, mycobacterium, tuberculosis, fumerate, malic acid, lyase
• 由来する生物種: Mycobacterium abscessus
• 細胞内の位置: Cytoplasm : B1MKP6
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 99820.92

構造登録者

Seattle Structural Genomics Center for Infectious Disease (SSGCID) (登録日: 2011-04-29, 公開日: 2011-05-11, 最終更新日: 2023-09-13)

主引用文献

Baugh, L.,Phan, I.,Begley, D.W.,Clifton, M.C.,Armour, B.,Dranow, D.M.,Taylor, B.M.,Muruthi, M.M.,Abendroth, J.,Fairman, J.W.,Fox, D.,Dieterich, S.H.,Staker, B.L.,Gardberg, A.S.,Choi, R.,Hewitt, S.N.,Napuli, A.J.,Myers, J.,Barrett, L.K.,Zhang, Y.,Ferrell, M.,Mundt, E.,Thompkins, K.,Tran, N.,Lyons-Abbott, S.,Abramov, A.,Sekar, A.,Serbzhinskiy, D.,Lorimer, D.,Buchko, G.W.,Stacy, R.,Stewart, L.J.,Edwards, T.E.,Van Voorhis, W.C.,Myler, P.J.
Increasing the structural coverage of tuberculosis drug targets.
Tuberculosis (Edinb), 95:142-148, 2015

PubMed Abstract: High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD <1 Å, >85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases.

PubMed: 25613812
DOI: 10.1016/j.tube.2014.12.003

実験手法

X-RAY DIFFRACTION (2.3 Å)