3mkl: Difference between revisions

Latest revision as of 06:29, 27 November 2024

Crystal structure of DNA-binding transcriptional dual regulator from Escherichia coli K-12

Structural highlights

3mkl is a 2 chain structure with sequence from Escherichia coli K-12. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.15Å
Ligands:	MSE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

GADX_ECOLI Positively regulates the expression of about fifteen genes involved in acid resistance such as gadA, gadB and gadC. Depending on the conditions (growth phase and medium), can repress gadW.^[1] ^[2] ^[3] ^[4] ^[5] ^[6]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

References

↑ Hommais F, Krin E, Laurent-Winter C, Soutourina O, Malpertuy A, Le Caer JP, Danchin A, Bertin P. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol Microbiol. 2001 Apr;40(1):20-36. PMID:11298273
↑ Tramonti A, Visca P, De Canio M, Falconi M, De Biase D. Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system. J Bacteriol. 2002 May;184(10):2603-13. PMID:11976288
↑ Ma Z, Richard H, Tucker DL, Conway T, Foster JW. Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW). J Bacteriol. 2002 Dec;184(24):7001-12. PMID:12446650
↑ Tucker DL, Tucker N, Ma Z, Foster JW, Miranda RL, Cohen PS, Conway T. Genes of the GadX-GadW regulon in Escherichia coli. J Bacteriol. 2003 May;185(10):3190-201. PMID:12730179
↑ Ma Z, Richard H, Foster JW. pH-Dependent modulation of cyclic AMP levels and GadW-dependent repression of RpoS affect synthesis of the GadX regulator and Escherichia coli acid resistance. J Bacteriol. 2003 Dec;185(23):6852-9. PMID:14617649
↑ Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P. GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli. Microbiology. 2004 Jan;150(Pt 1):61-72. PMID:14702398

Proteopedia Page Contributors and Editors (what is this?)

OCA

[1] Hommais F, Krin E, Laurent-Winter C, Soutourina O, Malpertuy A, Le Caer JP, Danchin A, Bertin P. Large-scale monitoring of pleiotropic regulation of gene expression by the prokaryotic nucleoid-associated protein, H-NS. Mol Microbiol. 2001 Apr;40(1):20-36. PMID:11298273

[2] Tramonti A, Visca P, De Canio M, Falconi M, De Biase D. Functional characterization and regulation of gadX, a gene encoding an AraC/XylS-like transcriptional activator of the Escherichia coli glutamic acid decarboxylase system. J Bacteriol. 2002 May;184(10):2603-13. PMID:11976288

[3] Ma Z, Richard H, Tucker DL, Conway T, Foster JW. Collaborative regulation of Escherichia coli glutamate-dependent acid resistance by two AraC-like regulators, GadX and GadW (YhiW). J Bacteriol. 2002 Dec;184(24):7001-12. PMID:12446650

[4] Tucker DL, Tucker N, Ma Z, Foster JW, Miranda RL, Cohen PS, Conway T. Genes of the GadX-GadW regulon in Escherichia coli. J Bacteriol. 2003 May;185(10):3190-201. PMID:12730179

[5] Ma Z, Richard H, Foster JW. pH-Dependent modulation of cyclic AMP levels and GadW-dependent repression of RpoS affect synthesis of the GadX regulator and Escherichia coli acid resistance. J Bacteriol. 2003 Dec;185(23):6852-9. PMID:14617649

[6] Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P. GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli. Microbiology. 2004 Jan;150(Pt 1):61-72. PMID:14702398

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[4]

[5]

[6]

@@ Line 1: / Line 1: @@
-{{STRUCTURE_3mkl|  PDB=3mkl  |  SCENE=  }}
-===Crystal structure of DNA-binding transcriptional dual regulator from Escherichia coli K-12===
-==About this Structure==
+==Crystal structure of DNA-binding transcriptional dual regulator from Escherichia coli K-12==
-[[3mkl]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MKL OCA].
+<StructureSection load='3mkl' size='340' side='right'caption='[[3mkl]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
-[[Category: Escherichia coli]]
+== Structural highlights ==
-[[Category: Chang, C.]]
+<table><tr><td colspan='2'>[[3mkl]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3MKL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3MKL FirstGlance]. <br>
-[[Category: Clancy, S.]]
+</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>
-[[Category: Joachimiak, A.]]
+<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>
-[[Category: MCSG, Midwest Center for Structural Genomics.]]
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3mkl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3mkl OCA], [https://pdbe.org/3mkl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3mkl RCSB], [https://www.ebi.ac.uk/pdbsum/3mkl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3mkl ProSAT]</span></td></tr>
-[[Category: Mack, J.]]
+</table>
-[[Category: Dna-binding protein]]
+== Function ==
-[[Category: Mcsg]]
+[https://www.uniprot.org/uniprot/GADX_ECOLI GADX_ECOLI] Positively regulates the expression of about fifteen genes involved in acid resistance such as gadA, gadB and gadC. Depending on the conditions (growth phase and medium), can repress gadW.<ref>PMID:11298273</ref> <ref>PMID:11976288</ref> <ref>PMID:12446650</ref> <ref>PMID:12730179</ref> <ref>PMID:14617649</ref> <ref>PMID:14702398</ref>
-[[Category: Midwest center for structural genomic]]
+== Evolutionary Conservation ==
-[[Category: Protein structure initiative]]
+[[Image:Consurf_key_small.gif|200px|right]]
-[[Category: Psi2]]
+Check<jmol>
-[[Category: Structural genomic]]
+  <jmolCheckbox>
-[[Category: Transcription regulator]]
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/mk/3mkl_consurf.spt"</scriptWhenChecked>
-[[Category: Transcriptional dual regulator]]
+    <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=3mkl ConSurf].
+<div style="clear:both"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli K-12]]
+[[Category: Large Structures]]
+[[Category: Chang C]]
+[[Category: Clancy S]]
+[[Category: Joachimiak A]]
+[[Category: Mack J]]

3mkl: Difference between revisions

Latest revision as of 06:29, 27 November 2024

Crystal structure of DNA-binding transcriptional dual regulator from Escherichia coli K-12

Structural highlights

Function

Evolutionary Conservation

References

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