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== | ==Crystal structure of the transcriptional factor from C.glutamicum at 2.2 angstrom resolution== | ||
<StructureSection load='2ek5' size='340' side='right'caption='[[2ek5]], [[Resolution|resolution]] 2.20Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2ek5]] is a 4 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=2EK5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2EK5 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=2ek5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ek5 OCA], [https://pdbe.org/2ek5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ek5 RCSB], [https://www.ebi.ac.uk/pdbsum/2ek5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ek5 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q8NLJ5_CORGL Q8NLJ5_CORGL] | |||
== 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/ek/2ek5_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=2ek5 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== 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. | 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. | ||
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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
[[Category: Corynebacterium glutamicum]] | <div class="pdbe-citations 2ek5" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: Gao | <references/> | ||
[[Category: Tanaka | __TOC__ | ||
[[Category: Yao | </StructureSection> | ||
[[Category: Corynebacterium glutamicum ATCC 13032]] | |||
[[Category: Large Structures]] | |||
[[Category: Gao YG]] | |||
[[Category: Tanaka I]] | |||
[[Category: Yao M]] | |||
Latest revision as of 10:57, 30 October 2024
Crystal structure of the transcriptional factor from C.glutamicum at 2.2 angstrom resolutionCrystal structure of the transcriptional factor from C.glutamicum at 2.2 angstrom resolution
Structural highlights
FunctionEvolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedAmong 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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