1q7t: Difference between revisions

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OCA

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 ==Rv1170 (MshB) from Mycobacterium tuberculosis==
-<StructureSection load='1q7t' size='340' side='right' caption='[[1q7t]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='1q7t' size='340' side='right'caption='[[1q7t]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1q7t]] is a 2 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=1Q7T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1Q7T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1q7t]] is a 2 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=1Q7T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q7T FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.9&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rv1170 (MshB) ([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=BOG:B-OCTYLGLUCOSIDE'>BOG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></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=1q7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q7t OCA], [http://pdbe.org/1q7t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1q7t RCSB], [http://www.ebi.ac.uk/pdbsum/1q7t PDBsum], [http://www.topsan.org/Proteins/TBSGC/1q7t TOPSAN]</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=1q7t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q7t OCA], [https://pdbe.org/1q7t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q7t RCSB], [https://www.ebi.ac.uk/pdbsum/1q7t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q7t ProSAT], [https://www.topsan.org/Proteins/TBSGC/1q7t TOPSAN]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/MSHB_MYCTO MSHB_MYCTO]] Catalyzes the deacetylation of 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside (GlcNAc-Ins) in the mycothiol (MSH) biosynthesis pathway. Shows some amidase activity toward S-conjugates of mycothiol (By similarity).
+[https://www.uniprot.org/uniprot/MSHB_MYCTU MSHB_MYCTU] Catalyzes the deacetylation of 1D-myo-inositol 2-acetamido-2-deoxy-alpha-D-glucopyranoside (GlcNAc-Ins) in the mycothiol (MSH) biosynthesis pathway. Shows some amidase activity toward S-conjugates of mycothiol.<ref>PMID:11092856</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
    <jmolCheckbox>
-     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q7/1q7t_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/q7/1q7t_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 19: / Line 20: @@
 </jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1q7t ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-All living species require protection against the damaging effects of the reactive oxygen species that are a natural by-product of aerobic life. In most organisms, glutathione is a critical component of these defences, maintaining a reducing environment inside cells. Some bacteria, however, including pathogenic mycobacteria, use an alternative low molecular mass thiol compound called mycothiol (MSH) for this purpose. Enzymes that synthesize MSH are attractive candidates for the design of novel anti-TB drugs because of the importance of MSH for mycobacterial life and the absence of such enzymes in humans. We have determined the three-dimensional structure of MshB (Rv1170), a metal-dependent deacetylase from Mycobacterium tuberculosis that catalyses the second step in MSH biosynthesis. The structure, determined at 1.9A resolution by X-ray crystallography (R=19.0%, R(free)=21.4%), reveals an alpha/beta fold in which helices pack against a seven-stranded mostly parallel beta-sheet. Large loops emanating from the C termini of the beta-strands enclose a deep cavity, which is the location of the putative active site. At the bottom of this cavity is a metal-binding site associated with a sequence motif AHPDDE that is invariant in all homologues. An adventitiously bound beta-octylglucoside molecule, used in crystallization, enables us to model the binding of the true substrate and propose a metal-dependent mechanistic model for deacetylation. Sequence comparisons indicate that MshB is representative of a wider family of enzymes that act on substituted N-acetylglucosamine residues, including a deacetylase involved in the biosynthesis of glycosylphosphatidylinositol (GPI) anchors in eukaryotes.
-Crystal structure of MshB from Mycobacterium tuberculosis, a deacetylase involved in mycothiol biosynthesis.,McCarthy AA, Peterson NA, Knijff R, Baker EN J Mol Biol. 2004 Jan 23;335(4):1131-41. PMID:14698305<ref>PMID:14698305</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1q7t" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Baker, E N]]
+[[Category: Large Structures]]
-[[Category: Knijff, R]]
+[[Category: Mycobacterium tuberculosis]]
-[[Category: McCarthy, A A]]
+[[Category: Baker EN]]
-[[Category: Peterson, N A]]
+[[Category: Knijff R]]
-[[Category: Structural genomic]]
+[[Category: McCarthy AA]]
-[[Category: Hydrolase]]
+[[Category: Peterson NA]]
-[[Category: Modified rossmann fold]]
-[[Category: PSI, Protein structure initiative]]
-[[Category: Tbsgc]]