2pud: Difference between revisions

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-[[Image:2pud.gif|left|200px]]
- {{Structure
+==CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES==
-|PDB= 2pud |SIZE=350|CAPTION= <scene name='initialview01'>2pud</scene>, resolution 2.600&Aring;
+<StructureSection load='2pud' size='340' side='right'caption='[[2pud]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</scene>
+<table><tr><td colspan='2'>[[2pud]] 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=2PUD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2PUD FirstGlance]. <br>
-|ACTIVITY=
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
-|GENE= PURR ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=562 Escherichia coli])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HPA:HYPOXANTHINE'>HPA</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=2pud FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pud OCA], [https://pdbe.org/2pud PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2pud RCSB], [https://www.ebi.ac.uk/pdbsum/2pud PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2pud 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/2pud_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=2pud ConSurf].
+<div style="clear:both"></div>
-'''CRYSTAL STRUCTURE OF THE LACI FAMILY MEMBER, PURR, BOUND TO DNA: MINOR GROOVE BINDING BY ALPHA HELICES'''
+==See Also==
+*[[Purine repressor|Purine repressor]]
+== References ==
-==Overview==
+<references/>
-The three-dimensional structure of a ternary complex of the purine repressor, PurR, bound to both its corepressor, hypoxanthine, and the 16-base pair purF operator site has been solved at 2.7 A resolution by x-ray crystallography. The bipartite structure of PurR consists of an amino-terminal DNA-binding domain and a larger carboxyl-terminal corepressor binding and dimerization domain that is similar to that of the bacterial periplasmic binding proteins. The DNA-binding domain contains a helix-turn-helix motif that makes base-specific contacts in the major groove of the DNA. Base contacts are also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove. Critical to hinge helix-minor groove binding is the intercalation of the side chains of Leu54 and its symmetry-related mate, Leu54', into the central CpG-base pair step. These residues thereby act as "leucine levers" to pry open the minor groove and kink the purF operator by 45 degrees.
+__TOC__
+</StructureSection>
-==About this Structure==
-PUD is a [[Single protein]] structure of 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=2PUD OCA].
-==Reference==
-Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices., Schumacher MA, Choi KY, Zalkin H, Brennan RG, Science. 1994 Nov 4;266(5186):763-70. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7973627 7973627]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Brennan, R G.]]
+[[Category: Brennan RG]]
-[[Category: Choi, K Y.]]
+[[Category: Choi KY]]
-[[Category: Schumacher, M A.]]
+[[Category: Schumacher MA]]
-[[Category: Zalkin, H.]]
+[[Category: Zalkin H]]
-[[Category: HPA]]
-[[Category: complex (dna-binding protein/dna)]]
-[[Category: dna-binding regulatory protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 18:17:28 2008''