3lap: Difference between revisions

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-{{Seed}}
-[[Image:3lap.jpg|left|200px]]
-<!--
+==The Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound to its DNA Operator and L-canavanine.==
-The line below this paragraph, containing "STRUCTURE_3lap", creates the "Structure Box" on the page.
+<StructureSection load='3lap' size='340' side='right'caption='[[3lap]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3lap]] is a 12 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=3LAP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3LAP FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.15&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GGB:L-CANAVANINE'>GGB</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3lap|  PDB=3lap  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3lap FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3lap OCA], [https://pdbe.org/3lap PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3lap RCSB], [https://www.ebi.ac.uk/pdbsum/3lap PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3lap ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ARGR_MYCTU ARGR_MYCTU] Regulates arginine biosynthesis genes (By similarity).
+== 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/la/3lap_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/main_output.php?pdb_ID=3lap ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The concentration of L-arginine in Mycobacterium tuberculosis (Mtb) and in many other bacteria is controlled by a transcriptional factor called the arginine repressor (ArgR). It regulates the transcription of the biosynthetic genes of the arginine operon by interacting with the approximately 16- to 20-bp ARG boxes in the promoter site of the operon. ArgRs in the arginine bound form are hexamers in which each protomer has two separately folded domains. The C-terminal domains form a hexameric core, whereas the N-terminal domains have the winged helix-turn-helix DNA-binding motif. Here, we present the crystal structure of the MtbArgR hexamer bound to three copies of the 16-bp DNA operator in the presence of trace amounts of L-arginine, determined to 2.15 A resolution. In contrast to our previously published structure of the ternary MtbArgR-DNA complex in the presence of 10 mM L-arginine, the DNA operators do not form a double ARG box in the structure reported here. The present structure not only retains the noncrystallographic 32 symmetry of the core (as in the earlier structure), but it also has the 3-fold axis for the whole complex. The core trimers are rotated relative to one another as in the other holo hexamers of MtbArgR, although the L-arginine ligands have only partial density and do not fully occupy the arginine-binding sites. Refinement of the occupancies and B-factors of ligands resulted in a value of approximately 4.4 arginine ligands per hexamer. This has allowed the dissociation constant of arginine from the arginine-binding site to be estimated. The present structure also has two protomer conformations, folded and extended. However, they are different from the conformations in the complex determined at an L-arginine concentration of 10 mM and do not form an interlocking arrangement. The new complex is less stable than the earlier described complex bound with nine arginine residues. Thus, the former can be considered as an intermediate in a pathway to the latter. On the basis of the structure of this intermediate complex, a more detailed mechanism of the arginine biosynthesis regulation in Mtb is proposed.
-===The Structure of the Intermediate Complex of the Arginine Repressor from Mycobacterium tuberculosis Bound to its DNA Operator and L-canavanine.===
+Crystal structure of the intermediate complex of the arginine repressor from Mycobacterium tuberculosis bound with its DNA operator reveals detailed mechanism of arginine repression.,Cherney LT, Cherney MM, Garen CR, James MN J Mol Biol. 2010 Jun 4;399(2):240-54. Epub 2010 Apr 9. PMID:20382162<ref>PMID:20382162</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3lap" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20382162}}, adds the Publication Abstract to the page
+*[[Arginine repressor 3D structures|Arginine repressor 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20382162 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20382162}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-LAP is a 12 chains structure with sequences 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=3LAP OCA].
+[[Category: Mycobacterium tuberculosis H37Rv]]
+[[Category: Cherney LT]]
-==Reference==
+[[Category: Cherney MM]]
-<ref group="xtra">PMID:20382162</ref><references group="xtra"/>
+[[Category: Garen CR]]
-[[Category: Mycobacterium tuberculosis]]
+[[Category: James MNG]]
-[[Category: Cherney, L T.]]
-[[Category: Cherney, M M.]]
-[[Category: Garen, C R.]]
-[[Category: James, M N.G.]]
-[[Category: TBSGC, TB Structural Genomics Consortium.]]
-[[Category: Amino-acid biosynthesis]]
-[[Category: Arginine biosynthesis]]
-[[Category: Arginine repressor]]
-[[Category: Argr-dna-canavanine ternary complex]]
-[[Category: Cytoplasm]]
-[[Category: Dna binding]]
-[[Category: Dna-binding]]
-[[Category: Mycobacterium tuberculosis]]
-[[Category: Mycobacterium tuberculosis structural proteomics project]]
-[[Category: Repressor]]
-[[Category: Structural genomic]]
-[[Category: Tb structural genomics consortium]]
-[[Category: Tbsgc]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-[[Category: Transcription regulator]]
-[[Category: Transcription regulator-dna complex]]
-[[Category: Xmtb]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May  5 11:56:16 2010''