2rbf: Difference between revisions

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-{{Seed}}
-[[Image:2rbf.png|left|200px]]
-<!--
+==Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2)==
-The line below this paragraph, containing "STRUCTURE_2rbf", creates the "Structure Box" on the page.
+<StructureSection load='2rbf' size='340' side='right'caption='[[2rbf]], [[Resolution|resolution]] 2.25&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[2rbf]] is a 4 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=2RBF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2RBF FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.25&#8491;</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=2rbf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2rbf OCA], [https://pdbe.org/2rbf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2rbf RCSB], [https://www.ebi.ac.uk/pdbsum/2rbf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2rbf ProSAT]</span></td></tr>
-{{STRUCTURE_2rbf|  PDB=2rbf  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PUTA_ECOLI PUTA_ECOLI] Oxidizes proline to glutamate for use as a carbon and nitrogen source and also function as a transcriptional repressor of the put operon.
+== 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/rb/2rbf_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=2rbf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The multifunctional Escherichia coli proline utilization A (PutA) flavoprotein functions both as a membrane-associated proline catabolic enzyme and as a transcriptional repressor of the proline utilization genes putA and putP. To better understand the mechanism of transcriptional regulation by PutA, we have mapped the put-regulatory region, determined a crystal structure of the PutA ribbon-helix-helix domain (PutA52, a polypeptide corresponding to residues 1-52 of E. coli PutA) complexed with DNA, and examined the thermodynamics of DNA binding to PutA52. Five operator sites, each containing the sequence motif 5'-GTTGCA-3', were identified using gel-shift analysis. Three of the sites are shown to be critical for repression of putA, whereas the two other sites are important for repression of putP. The 2.25-A-resolution crystal structure of PutA52 bound to one of the operators (operator 2; 21 bp) shows that the protein contacts a 9-bp fragment corresponding to the GTTGCA consensus motif plus three flanking base pairs. Since the operator sequences differ in flanking bases, the structure implies that PutA may have different affinities for the five operators. This hypothesis was explored using isothermal titration calorimetry. The binding of PutA52 to operator 2 is exothermic, with an enthalpy of -1.8 kcal/mol and a dissociation constant of 210 nM. Substitution of the flanking bases of operator 4 into operator 2 results in an unfavorable enthalpy of 0.2 kcal/mol and a 15-fold-lower affinity, showing that base pairs outside of the consensus motif impact binding. Structural and thermodynamic data suggest that hydrogen bonds between Lys9 and bases adjacent to the GTTGCA motif contribute to transcriptional regulation by fine-tuning the affinity of PutA for put control operators.
-===Structure of the ribbon-helix-helix domain of Escherichia coli PutA (PutA52) complexed with operator DNA (O2)===
+Structural basis of the transcriptional regulation of the proline utilization regulon by multifunctional PutA.,Zhou Y, Larson JD, Bottoms CA, Arturo EC, Henzl MT, Jenkins JL, Nix JC, Becker DF, Tanner JJ J Mol Biol. 2008 Aug 1;381(1):174-88. Epub 2008 Jun 7. PMID:18586269<ref>PMID:18586269</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2rbf" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18586269}}, adds the Publication Abstract to the page
+*[[Proline utilization A|Proline utilization A]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18586269 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18586269}}
+__TOC__
+</StructureSection>
-==About this Structure==
-RBF is a 4 chains structure of sequences 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=2RBF OCA].
-==Reference==
-<ref group="xtra">PMID:18586269</ref><references group="xtra"/>
 [[Category: Escherichia coli]]
-[[Category: Tanner, J J.]]
+[[Category: Large Structures]]
-[[Category: Dna-binding]]
+[[Category: Tanner JJ]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: Multifunctional enzyme]]
-[[Category: Nad]]
-[[Category: Oxidoreductase]]
-[[Category: Oxidoreductase/dna complex]]
-[[Category: Proline metabolism]]
-[[Category: Proline utilization some]]
-[[Category: Protein-dna complex]]
-[[Category: Puta]]
-[[Category: Repressor]]
-[[Category: Ribbon-helix-helix]]
-[[Category: Transcription]]
-[[Category: Transcription regulation]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Feb 16 11:36:55 2009''