2puf: Difference between revisions

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-[[Image:2puf.gif|left|200px]]<br /><applet load="2puf" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2puf, resolution 3.000&Aring;" />
-'''CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES'''<br />
-==Overview==
+==CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES==
-Guanine or hypoxanthine, physiological corepressors of the Escherichia, coli purine repressor (PurR), promote formation of the ternary, PurR-corepressor-operator DNA complex that functions to repress pur operon, gene expression. Structure-based predictions on the importance of Arg190, in determining 6-oxopurine specificity and corepressor binding affinity, were tested by mutagenesis, analysis of in vivo function, and in vitro, corepressor binding measurements. Replacements of Arg190 with Ala or Gln, resulted in functional repressors in which binding of guanine and, hypoxanthine was retained but specificity was relaxed to permit binding of, adenine. X-ray structures were determined for ternary complexes of mutant, repressors with purines (adenine, guanine, hypoxanthine, and, 6-methylpurine) and operator DNA. These structures indicate that R190A, binds guanine, hypoxanthine, and adenine with nearly equal, albeit, reduced, affinity in large part because of a newly made compensatory, hydrogen bond between the rotated hydroxyl side chain of Ser124 and the, exocyclic 6 positions of the purines. Through direct and water-mediated, contacts, the R190Q protein binds adenine with a nearly 75-fold higher, affinity than the wild type repressor while maintaining wild type affinity, for guanine and hypoxanthine. The results establish at the atomic level, the basis for the critical role of Arg190 in the recognition of the, exocyclic 6 position of its purine corepressors and the successful, redesign of corepressor specificity.
+<StructureSection load='2puf' size='340' side='right'caption='[[2puf]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2puf]] 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=2PUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUF 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]] 3&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GUN:GUANINE'>GUN</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=2puf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2puf OCA], [https://pdbe.org/2puf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2puf RCSB], [https://www.ebi.ac.uk/pdbsum/2puf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2puf 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/pu/2puf_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=2puf ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-PUF 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 GUN as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2PUF OCA].
+*[[Purine repressor|Purine repressor]]
+== References ==
-==Reference==
+<references/>
-Structure-based redesign of corepressor specificity of the Escherichia coli purine repressor by substitution of residue 190., Lu F, Schumacher MA, Arvidson DN, Haldimann A, Wanner BL, Zalkin H, Brennan RG, Biochemistry. 1998 Jan 27;37(4):971-82. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9454587 9454587]
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Arvidson, D.N.]]
+[[Category: Arvidson DN]]
-[[Category: Brennan, R.G.]]
+[[Category: Brennan RG]]
-[[Category: Haldimann, A.]]
+[[Category: Haldimann A]]
-[[Category: Lu, F.]]
+[[Category: Lu F]]
-[[Category: Schumacher, M.A.]]
+[[Category: Schumacher MA]]
-[[Category: Wanner, B.L.]]
+[[Category: Wanner BL]]
-[[Category: Zalkin, H.]]
+[[Category: Zalkin H]]
-[[Category: GUN]]
-[[Category: complex (dna-binding protein/dna)]]
-[[Category: dna-binding regulatory protein]]
-[[Category: extended corepressor specificity]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 13:40:39 2007''