2du9: Difference between revisions

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{{Seed}}
[[Image:2du9.png|left|200px]]


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==crystal structure of the transcriptional factor from C.glutamicum==
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<StructureSection load='2du9' size='340' side='right'caption='[[2du9]], [[Resolution|resolution]] 2.28&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2du9]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_glutamicum_ATCC_13032 Corynebacterium glutamicum ATCC 13032]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DU9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DU9 FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.28&#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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
{{STRUCTURE_2du9|  PDB=2du9  |  SCENE=  }}
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2du9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2du9 OCA], [https://pdbe.org/2du9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2du9 RCSB], [https://www.ebi.ac.uk/pdbsum/2du9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2du9 ProSAT]</span></td></tr>
</table>
== 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/du/2du9_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2du9 ConSurf].
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== Publication Abstract from PubMed ==
Among the transcription factors, the helix-turn-helix (HTH) GntR family comprised of FadR, HutC, MocR, YtrA, AraR, and PlmA subfamilies regulates the most varied biological processes. Generally, proteins belonging to this family contain an N-terminal DNA-binding domain and a C-terminal effector-binding/oligomerization domain. The members of the YtrA subfamily are much shorter than other members of this family, with chain lengths of 120-130 residues with about 50 residues located in the C-terminal domain. Because of this length, the mode of dimerization and the ability to bind effectors by the C-terminal domain are puzzling. Here, we first report the structure of the transcription factor CGL2947 from Corynebacterium glutamicum, which belongs to the YtrA family. The monomer is composed of a DNA-binding domain containing a winged HTH motif in the N terminus and two helices (alpha4 and alpha5) with a fishhook-shaped arrangement in the C terminus. Helices alpha4 and alpha5 of two monomers intertwine together to form a novel homodimer assembly. The effector-accommodating pocket with 2-methyl-2,4-pentanediol (MPD) docked was located, and it was suggested to represent a novel mode of effector binding. The structures in two crystal forms (MPD-free and -bound in the proposed effector-binding pocket) were solved. The structural variations have implications regarding how the effector-induced conformational change modulates DNA affinity for YtrA family members.


===crystal structure of the transcriptional factor from C.glutamicum===
The structures of transcription factor CGL2947 from Corynebacterium glutamicum in two crystal forms: a novel homodimer assembling and the implication for effector-binding mode.,Gao YG, Yao M, Itou H, Zhou Y, Tanaka I Protein Sci. 2007 Sep;16(9):1878-86. PMID:17766384<ref>PMID:17766384</ref>


 
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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(as it appears on PubMed at http://www.pubmed.gov), where 17766384 is the PubMed ID number.
== References ==
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<references/>
{{ABSTRACT_PUBMED_17766384}}
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</StructureSection>
==About this Structure==
[[Category: Corynebacterium glutamicum ATCC 13032]]
2DU9 is a 1 chain structure of sequence from [http://en.wikipedia.org/wiki/Corynebacterium_glutamicum Corynebacterium glutamicum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DU9 OCA].
[[Category: Large Structures]]
 
[[Category: Gao Y]]
==Reference==
[[Category: Tanaka I]]
<ref group="xtra">PMID:17766384</ref><references group="xtra"/>
[[Category: Yao M]]
[[Category: Corynebacterium glutamicum]]
[[Category: Gao, Y.]]
[[Category: Tanaka, I.]]
[[Category: Yao, M.]]
[[Category: Winged helix-turn-helix]]
 
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