4IZ9

Crystal structure of an acetate kinase from Mycobacterium avium bound to an unknown acid-ApCpp conjugate and manganese

Summary for 4IZ9

• Entry DOI: 10.2210/pdb4iz9/pdb
• Related: 3p4i 3r9p 4dq8 4ijn
• Descriptor: Acetate kinase, MANGANESE (II) ION, DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER, ... (6 entities in total)
• Functional Keywords: structural genomics, seattle structural genomics center for infectious disease, ssgcid, acka, propionate kinase, acid-kinase, atp-dependent, non-hydrolyzable atp analog, anomalous manganese signal, unknown conjugate, transferase
• Biological source: Mycobacterium avium
• Cellular location: Cytoplasm : A0QLU8
• Total number of polymer chains: 1
• Total formula weight: 42577.56

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID) (deposition date: 2013-01-29, release date: 2013-02-20, Last modification date: 2023-09-20)

Primary citation

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

Experimental method

X-RAY DIFFRACTION (1.98 Å)