2vpr: Difference between revisions

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[[Image:2vpr.png|left|200px]]


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==Tet repressor class H in complex with 5a,6- anhydrotetracycline-Mg==
The line below this paragraph, containing "STRUCTURE_2vpr", creates the "Structure Box" on the page.
<StructureSection load='2vpr' size='340' side='right'caption='[[2vpr]], [[Resolution|resolution]] 2.49&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'>[[2vpr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pasteurella_multocida Pasteurella multocida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VPR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VPR 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]] 2.49&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TDC:5A,6-ANHYDROTETRACYCLINE'>TDC</scene></td></tr>
{{STRUCTURE_2vpr|  PDB=2vpr  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vpr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vpr OCA], [https://pdbe.org/2vpr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vpr RCSB], [https://www.ebi.ac.uk/pdbsum/2vpr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vpr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/TETR8_PASMD TETR8_PASMD] TetR is the repressor of the tetracycline resistance element; its N-terminal region forms a helix-turn-helix structure and binds DNA. Binding of tetracycline to TetR reduces the repressor affinity for the tetracycline resistance gene (tetA) promoter operator sites.
== 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/vp/2vpr_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=2vpr ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The Tet repressor (TetR) mediates the most important mechanism of bacterial resistance against tetracycline (Tc) antibiotics. In the absence of Tc, TetR is tightly bound to its operator DNA; upon binding of Tc with an associated Mg(2+) ion, it dissociates from the DNA, allowing expression of the repressed genes. Its tight control by Tc makes TetR broadly useful in genetic engineering. The Tc binding site is over 20 A from the DNA, so the binding signal must propagate a long distance. We use molecular dynamics simulations and continuum electrostatic calculations to test two models of the allosteric mechanism. We simulate the TetR:DNA complex, the Tc-bound, "induced" TetR, and the transition pathway between them. The simulations support the model inferred previously from the crystal structures and reveal new details. When [Tc:Mg](+) binds, the Mg(2+) ion makes direct and water-mediated interactions with helix 8 of one TetR monomer and helix 6 of the other monomer, and helix 6 is pulled in towards the central core of the structure. Hydrophobic interactions with helix 6 then pull helix 4 in a pendulum motion, with a maximal displacement at its N-terminus: the DNA interface. The crystal structure of an additional TetR reported here corroborates this motion. The N-terminal residue of helix 4, Lys48, is highly conserved in DNA-binding regulatory proteins of the TetR class and makes the largest contribution of any amino acid to the TetR:DNA binding free energy. Thus, the conformational changes lead to a drastic reduction in the TetR:DNA binding affinity, allowing TetR to detach itself from the DNA. Tc plays the role of a specific Mg(2+) carrier, whereas the Mg(2+) ion itself makes key interactions that trigger the allosteric transition in the TetR:Tc complex.


===TET REPRESSOR CLASS H IN COMPLEX WITH 5A,6-ANHYDROTETRACYCLINE-MG===
Tet repressor induction by tetracycline: a molecular dynamics, continuum electrostatics, and crystallographic study.,Aleksandrov A, Schuldt L, Hinrichs W, Simonson T J Mol Biol. 2008 May 9;378(4):898-912. Epub 2008 Mar 19. PMID:18395746<ref>PMID:18395746</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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<div class="pdbe-citations 2vpr" style="background-color:#fffaf0;"></div>
(as it appears on PubMed at http://www.pubmed.gov), where 18395746 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_18395746}}
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</StructureSection>
==About this Structure==
[[Category: Large Structures]]
[[2vpr]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Pasteurella_multocida Pasteurella multocida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VPR OCA].
 
==Reference==
<ref group="xtra">PMID:18395746</ref><ref group="xtra">PMID:10700280</ref><ref group="xtra">PMID:8153629</ref><references group="xtra"/>
[[Category: Pasteurella multocida]]
[[Category: Pasteurella multocida]]
[[Category: Hinrichs, W.]]
[[Category: Hinrichs W]]
[[Category: Palm, G.]]
[[Category: Palm G]]
[[Category: Schuldt, L.]]
[[Category: Schuldt L]]
[[Category: Antibiotic resistance]]
[[Category: Dna-binding]]
[[Category: Magnesium]]
[[Category: Metal-binding]]
[[Category: Plasmid]]
[[Category: Repressor]]
[[Category: Transcription]]
[[Category: Transcription regulation]]
[[Category: Transcription regulator]]
Retrieved from "https://proteopedia.org/2vpr"