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| | <StructureSection load='3r2n' size='340' side='right'caption='[[3r2n]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='3r2n' size='340' side='right'caption='[[3r2n]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3r2n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Myclb Myclb]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R2N FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3r2n]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_leprae_Br4923 Mycobacterium leprae Br4923]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3R2N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3R2N FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ijf|3ijf]], [[3mpz|3mpz]]</div></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">cdd, MLBr02174 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561304 MYCLB])</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=3r2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r2n OCA], [https://pdbe.org/3r2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r2n RCSB], [https://www.ebi.ac.uk/pdbsum/3r2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r2n ProSAT]</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=3r2n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3r2n OCA], [https://pdbe.org/3r2n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3r2n RCSB], [https://www.ebi.ac.uk/pdbsum/3r2n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3r2n ProSAT]</span></td></tr> |
| | </table> | | </table> |
| - | <div style="background-color:#fffaf0;">
| + | == Function == |
| - | == Publication Abstract from PubMed == | + | [https://www.uniprot.org/uniprot/A0A0H3MRL9_MYCLB A0A0H3MRL9_MYCLB] This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.[ARBA:ARBA00003949][RuleBase:RU364006] |
| - | 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 Calpha RMSD <1 A, >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.
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| - | Increasing the structural coverage of tuberculosis drug targets.,Baugh L, Phan I, Begley DW, Clifton MC, Armour B, Dranow DM, Taylor BM, Muruthi MM, Abendroth J, Fairman JW, Fox D 3rd, Dieterich SH, Staker BL, Gardberg AS, Choi R, Hewitt SN, Napuli AJ, Myers J, Barrett LK, Zhang Y, Ferrell M, Mundt E, Thompkins K, Tran N, Lyons-Abbott S, Abramov A, Sekar A, Serbzhinskiy D, Lorimer D, Buchko GW, Stacy R, Stewart LJ, Edwards TE, Van Voorhis WC, Myler PJ Tuberculosis (Edinb). 2014 Dec 19. pii: S1472-9792(14)20565-8. doi:, 10.1016/j.tube.2014.12.003. PMID:25613812<ref>PMID:25613812</ref>
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| - | | + | |
| - | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
| + | |
| - | </div>
| + | |
| - | <div class="pdbe-citations 3r2n" style="background-color:#fffaf0;"></div>
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| | | | |
| | ==See Also== | | ==See Also== |
| | *[[Deaminase 3D structures|Deaminase 3D structures]] | | *[[Deaminase 3D structures|Deaminase 3D structures]] |
| - | == References == | |
| - | <references/> | |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Myclb]] | + | [[Category: Mycobacterium leprae Br4923]] |
| - | [[Category: Structural genomic]]
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| - | [[Category: Catalytic zinc]]
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| - | [[Category: Cda]]
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| - | [[Category: Cytidine deaminase]]
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| - | [[Category: Drug resistance]]
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| - | [[Category: Homotetramer]]
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| - | [[Category: Hydrolase]]
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| - | [[Category: Pyrimidine salvage]]
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| - | [[Category: Ssgcid]]
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| - | [[Category: Tuberculosis]]
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| - | [[Category: Zinc binding protein]]
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