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| | ==Crystal structure of Mycobacterium tuberculosis malate synthase in complex with Methoxynaphthyldiketoacid== | | ==Crystal structure of Mycobacterium tuberculosis malate synthase in complex with Methoxynaphthyldiketoacid== |
| - | <StructureSection load='6c7b' size='340' side='right' caption='[[6c7b]], [[Resolution|resolution]] 2.13Å' scene=''> | + | <StructureSection load='6c7b' size='340' side='right'caption='[[6c7b]], [[Resolution|resolution]] 2.13Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6c7b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_tuberculosis"_(zopf_1883)_klein_1884 "bacillus tuberculosis" (zopf 1883) klein 1884]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C7B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6C7B FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6c7b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6C7B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6C7B FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ENY:(2Z)-2-hydroxy-4-(6-methoxynaphthalen-2-yl)-4-oxobut-2-enoic+acid'>ENY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.133Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">glcB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 "Bacillus tuberculosis" (Zopf 1883) Klein 1884])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ENY:(2Z)-2-hydroxy-4-(6-methoxynaphthalen-2-yl)-4-oxobut-2-enoic+acid'>ENY</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Malate_synthase Malate synthase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.3.9 2.3.3.9] </span></td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6c7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c7b OCA], [https://pdbe.org/6c7b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6c7b RCSB], [https://www.ebi.ac.uk/pdbsum/6c7b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6c7b ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6c7b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6c7b OCA], [http://pdbe.org/6c7b PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6c7b RCSB], [http://www.ebi.ac.uk/pdbsum/6c7b PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6c7b ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/A0A045ITM4_MYCTX A0A045ITM4_MYCTX]] Involved in the glycolate utilization. Catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA.[HAMAP-Rule:MF_00641][SAAS:SAAS00078445] | + | [https://www.uniprot.org/uniprot/MASZ_MYCTU MASZ_MYCTU] Involved in the glycolate utilization. Catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA (By similarity).[HAMAP-Rule:MF_00641] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6c7b" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6c7b" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Malate synthase 3D structures|Malate synthase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Malate synthase]] | + | [[Category: Large Structures]] |
| - | [[Category: Krieger, I V]] | + | [[Category: Mycobacterium tuberculosis]] |
| - | [[Category: Sacchettini, J C]] | + | [[Category: Krieger IV]] |
| - | [[Category: Structural genomic]] | + | [[Category: Sacchettini JC]] |
| - | [[Category: Acetyltransferase]]
| + | |
| - | [[Category: Tbsgc]]
| + | |
| - | [[Category: Transferase]]
| + | |
| - | [[Category: Transferase-transferase inhibitor complex]]
| + | |
| Structural highlights
Function
MASZ_MYCTU Involved in the glycolate utilization. Catalyzes the condensation and subsequent hydrolysis of acetyl-coenzyme A (acetyl-CoA) and glyoxylate to form malate and CoA (By similarity).[HAMAP-Rule:MF_00641]
Publication Abstract from PubMed
Human infection by Mycobacterium tuberculosis (Mtb) continues to be a global epidemic. Computer-aided drug design (CADD) methods are used to accelerate traditional drug discovery efforts. One non-covalent interaction that is being increasingly identified in biological systems but is neglected in CADD is the anion-pi interaction. The study reported herein supports the conclusion that anion-pi interactions play a central role in directing the binding of phenyl-diketo acid (PDKA) inhibitors to malate synthase (GlcB), an enzyme required for Mycobacterium tuberculosis virulence. Using density functional theory methods (M06-2X/6-31+G(d)), a GlcB active site template was developed for a predictive model through a comparative analysis of PDKA-bound GlcB crystal structures. The active site model includes the PDKA molecule and the protein determinants of the electrostatic, hydrogen-bonding, and anion-pi interactions involved in binding. The predictive model accurately determines the Asp 633-PDKA structural position upon binding, and precisely predicts the relative binding enthalpies of a series of 2-ortho halide-PDKAs to GlcB. A screening model was also developed to efficiently assess the propensity of each PDKA analog to participate in an anion-pi interaction; this method is in good agreement with both the predictive model and the experimental binding enthalpies for the 2-ortho halide-PDKAs. With the screening and predictive models in hand, we have developed an efficient method for computationally screening and evaluating the binding enthalpy of variously substituted PDKA molecules. This study serves to illustrate the contribution of this overlooked interaction to binding affinity and demonstrates the importance of integrating anion-pi interactions into structure-based CADD.
Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids.,Ellenbarger J, Krieger I, Huang HL, Gomez-Coca S, Ioerger TR, Sacchettini JC, Wheeler SE, Dunbar KR J Chem Inf Model. 2018 Aug 23. doi: 10.1021/acs.jcim.8b00417. PMID:30137983[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ellenbarger J, Krieger I, Huang HL, Gomez-Coca S, Ioerger TR, Sacchettini JC, Wheeler SE, Dunbar KR. Anion-pi Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids. J Chem Inf Model. 2018 Aug 23. doi: 10.1021/acs.jcim.8b00417. PMID:30137983 doi:http://dx.doi.org/10.1021/acs.jcim.8b00417
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