1dbq: Difference between revisions

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New page: left|200px<br /><applet load="1dbq" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dbq, resolution 2.2Å" /> '''DNA-BINDING REGULATOR...
 
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'''DNA-BINDING REGULATORY PROTEIN'''<br />


==Overview==
==DNA-BINDING REGULATORY PROTEIN==
The modulation of the affinity of DNA-binding proteins by small molecule, effectors for cognate DNA sites is common to both prokaryotes and, eukaryotes. However, the mechanisms by which effector binding to one, domain affects DNA binding by a distal domain are poorly understood, structurally. In initial studies to provide insight into the mechanism of, effector-modulated DNA binding of the lactose repressor family, we, determined the crystal structure of the purine repressor bound to a, corepressor and purF operator. To extend our understanding, we have, determined the structure of the corepressor-free corepressor-binding, domain of the purine repressor at 2.2 A resolution. In the unliganded, state, structural changes in the corepressor-binding pocket cause each, subunit to rotate open by as much as 23 degrees, the consequences of which, are the disengagement of the minor groove-binding hinge helices and, repressor-DNA dissociation.
<StructureSection load='1dbq' size='340' side='right'caption='[[1dbq]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dbq]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1DBQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBQ 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]] 2.2&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1dbq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbq OCA], [https://pdbe.org/1dbq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbq RCSB], [https://www.ebi.ac.uk/pdbsum/1dbq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbq ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/PURR_ECOLI PURR_ECOLI] Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. In addition, it participates in the regulation or coregulation of genes involved in de novo pyrimidine nucleotide biosynthesis, salvage and uptake (pyrC, pyrD, carAB and codBA), and of several genes encoding enzymes necessary for nucleotide and polyamine biosynthesis (prsA, glyA, gcvTHP, speA, glnB). Binds to a 16-bp palindromic sequence located within the promoter region of pur regulon genes. The consensus binding sequence is 5'-ACGCAAACGTTTTCNT-3'. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression.<ref>PMID:2404765</ref> <ref>PMID:2211500</ref> <ref>PMID:1400170</ref> <ref>PMID:14741201</ref>
== 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/db/1dbq_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=1dbq ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1DBQ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with MG as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DBQ OCA].
*[[Purine repressor|Purine repressor]]
 
== References ==
==Reference==
<references/>
Mechanism of corepressor-mediated specific DNA binding by the purine repressor., Schumacher MA, Choi KY, Lu F, Zalkin H, Brennan RG, Cell. 1995 Oct 6;83(1):147-55. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7553867 7553867]
__TOC__
</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Brennan, R.G.]]
[[Category: Brennan RG]]
[[Category: Choi, K.Y.]]
[[Category: Choi KY]]
[[Category: Lu, F.]]
[[Category: Lu F]]
[[Category: Schumacher, M.A.]]
[[Category: Schumacher MA]]
[[Category: Zalkin, H.]]
[[Category: Zalkin H]]
[[Category: MG]]
[[Category: dna-binding regulatory protein]]
[[Category: purine repressor]]
[[Category: transcription regulation]]
 
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:08:36 2007''

Latest revision as of 09:51, 7 February 2024

DNA-BINDING REGULATORY PROTEINDNA-BINDING REGULATORY PROTEIN

Structural highlights

1dbq is a 2 chain structure with sequence from Escherichia coli. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.2Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PURR_ECOLI Is the main repressor of the genes involved in the de novo synthesis of purine nucleotides, regulating purB, purC, purEK, purF, purHD, purL, purMN and guaBA expression. In addition, it participates in the regulation or coregulation of genes involved in de novo pyrimidine nucleotide biosynthesis, salvage and uptake (pyrC, pyrD, carAB and codBA), and of several genes encoding enzymes necessary for nucleotide and polyamine biosynthesis (prsA, glyA, gcvTHP, speA, glnB). Binds to a 16-bp palindromic sequence located within the promoter region of pur regulon genes. The consensus binding sequence is 5'-ACGCAAACGTTTTCNT-3'. PurR is allosterically activated to bind its cognate DNA by binding the purine corepressors, hypoxanthine or guanine, thereby effecting transcription repression.[1] [2] [3] [4]

Evolutionary Conservation

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

See Also

References

  1. ↑ Meng LM, Kilstrup M, Nygaard P. Autoregulation of PurR repressor synthesis and involvement of purR in the regulation of purB, purC, purL, purMN and guaBA expression in Escherichia coli. Eur J Biochem. 1990 Jan 26;187(2):373-9. PMID:2404765
  2. ↑ Rolfes RJ, Zalkin H. Purification of the Escherichia coli purine regulon repressor and identification of corepressors. J Bacteriol. 1990 Oct;172(10):5637-42. PMID:2211500
  3. ↑ Choi KY, Zalkin H. Structural characterization and corepressor binding of the Escherichia coli purine repressor. J Bacteriol. 1992 Oct;174(19):6207-14. PMID:1400170
  4. ↑ Devroede N, Thia-Toong TL, Gigot D, Maes D, Charlier D. Purine and pyrimidine-specific repression of the Escherichia coli carAB operon are functionally and structurally coupled. J Mol Biol. 2004 Feb 6;336(1):25-42. PMID:14741201

1dbq, resolution 2.20Å

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