3isp: Difference between revisions

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 ==Crystal structure of ArgP from Mycobacterium tuberculosis==
-<StructureSection load='3isp' size='340' side='right' caption='[[3isp]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
+<StructureSection load='3isp' size='340' side='right'caption='[[3isp]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3isp]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycobacterium_tuberculosis Mycobacterium tuberculosis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ISP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3ISP FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3isp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3ISP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3ISP FirstGlance]. <br>
-</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Rv1985c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1773 Mycobacterium tuberculosis])</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]] 2.7&#8491;</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=3isp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3isp OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3isp RCSB], [http://www.ebi.ac.uk/pdbsum/3isp PDBsum]</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=3isp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3isp OCA], [https://pdbe.org/3isp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3isp RCSB], [https://www.ebi.ac.uk/pdbsum/3isp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3isp ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LYSG_MYCTU LYSG_MYCTU] Positively regulates the expression of the exporter LysE and represses its own expression. Activity requires the presence of a coinducer, lysine or histidine. Acts by binding to lysG-lysE promoter region. Also up-regulates the expression of ppsB, ppsC and ppsD, by binding to the upstream region of ppsB.<ref>PMID:29049397</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/is/3isp_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/is/3isp_consurf.spt"</scriptWhenChecked>
      <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=3isp ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Mycobacterium tuberculosis presents a challenging medical problem partly due to its persistent nonreplicative state. The inhibitor of chromosomal replication (iciA) protein encoded by M. tuberculosis has been suggested to inhibit chromosome replication initiation in vitro. However, iciA has also been identified as arginine permease (ArgP), a regulatory transcription factor for arginine outward transport. In order to understand the function of ArgP, we have determined its crystal structure by X-ray crystallography to a resolution of 2.7 A. ArgP is a member of the LysR-type transcriptional regulators (LTTRs) and forms a homodimer with each subunit containing two domains: a DNA binding domain (DBD) and a regulatory domain (RD). Two conformationally distinct subunits were identified: closed subunit and open subunit. This phenomenon was first observed in LTTR CbnR, but not in LTTR CrgA, and might be common in LTTRs. We identified two forms of dimers: DBD-type dimers and RD-type dimers. The former is confirmed in solution, and the latter is considered to form oligomers during function. We provide the first structural insights into the interaction of the extreme C-terminal residues with the DBD, which is confirmed by mutagenesis and analytical ultracentrifugation to be important for stability of the functional dimer. The structure serves as a model to suggest how three critical aspects, namely, DNA binding, homo-oligomerization, and interaction with RNAP, are mediated during regulation processing. A model is proposed for the LysR family of dimeric regulators.
-Crystal structure of ArgP from Mycobacterium tuberculosis confirms two distinct conformations of full-length LysR transcriptional regulators and reveals its function in DNA binding and transcriptional regulation.,Zhou X, Lou Z, Fu S, Yang A, Shen H, Li Z, Feng Y, Bartlam M, Wang H, Rao Z J Mol Biol. 2010 Mar 5;396(4):1012-24. Epub 2009 Dec 28. PMID:20036253<ref>PMID:20036253</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Mycobacterium tuberculosis]]
+[[Category: Large Structures]]
-[[Category: Bartlam, M]]
+[[Category: Mycobacterium tuberculosis H37Rv]]
-[[Category: Lou, Z]]
+[[Category: Bartlam M]]
-[[Category: Rao, Z]]
+[[Category: Lou Z]]
-[[Category: Sheng, F]]
+[[Category: Rao Z]]
-[[Category: Wang, H]]
+[[Category: Sheng F]]
-[[Category: Zhou, X]]
+[[Category: Wang H]]
-[[Category: Dna binding domain]]
+[[Category: Zhou X]]
-[[Category: Dna-binding]]
-[[Category: Regulatory domain]]
-[[Category: Rod shaped structure]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]