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| ==Crystal structure of a tRNA-guanine-N1-methyltransferase from Mycobacterium abscessus== | | ==Crystal structure of a tRNA-guanine-N1-methyltransferase from Mycobacterium abscessus== |
| <StructureSection load='3quv' size='340' side='right' caption='[[3quv]], [[Resolution|resolution]] 1.70Å' scene=''> | | <StructureSection load='3quv' size='340' side='right'caption='[[3quv]], [[Resolution|resolution]] 1.70Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[3quv]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Myca9 Myca9]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QUV OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3QUV FirstGlance]. <br> | | <table><tr><td colspan='2'>[[3quv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacteroides_abscessus_ATCC_19977 Mycobacteroides abscessus ATCC 19977]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QUV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QUV FirstGlance]. <br> |
| </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</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]] 1.7Å</td></tr> |
| <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MAB_3226c, trmD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=561007 MYCA9])</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></td></tr> |
| <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Transferase Transferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.1.1.221 and 2.1.1.228 2.1.1.221 and 2.1.1.228] </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=3quv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3quv OCA], [https://pdbe.org/3quv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3quv RCSB], [https://www.ebi.ac.uk/pdbsum/3quv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3quv 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=3quv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3quv OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3quv RCSB], [http://www.ebi.ac.uk/pdbsum/3quv PDBsum]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9]] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552] | | [https://www.uniprot.org/uniprot/B1MDI3_MYCA9 B1MDI3_MYCA9] Specifically methylates guanosine-37 in various tRNAs.[HAMAP-Rule:MF_00605][RuleBase:RU003464][SAAS:SAAS00040552] |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| 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>
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| </div>
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| ==See Also== | | ==See Also== |
| *[[TRNA methyltransferase|TRNA methyltransferase]] | | *[[TRNA methyltransferase 3D structures|TRNA methyltransferase 3D structures]] |
| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Myca9]] | | [[Category: Large Structures]] |
| [[Category: Transferase]] | | [[Category: Mycobacteroides abscessus ATCC 19977]] |
| [[Category: Structural genomic]]
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| [[Category: Chronic lung disease]]
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| [[Category: Domain swap]]
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| [[Category: Protein knot]]
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| [[Category: S-adenosyl-homocysteine]]
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| [[Category: S-adenosyl-methionine]]
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| [[Category: Sah]]
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| [[Category: Sam]]
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| [[Category: Ssgcid]]
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| [[Category: Sssgcid]]
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| [[Category: Trmd]]
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| [[Category: Trna methyltransferase]]
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