1zme

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[[Image:1zme.gif|left|200px]]
 
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==CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX==
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The line below this paragraph, containing "STRUCTURE_1zme", creates the "Structure Box" on the page.
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<StructureSection load='1zme' size='340' side='right'caption='[[1zme]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1zme]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZME OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ZME FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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{{STRUCTURE_1zme| PDB=1zme | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1zme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zme OCA], [https://pdbe.org/1zme PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1zme RCSB], [https://www.ebi.ac.uk/pdbsum/1zme PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1zme ProSAT]</span></td></tr>
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</table>
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'''CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX'''
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== Function ==
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[https://www.uniprot.org/uniprot/PUT3_YEAST PUT3_YEAST] Positive activator of the proline utilization pathway. Binds to the promoters of PUT1 and PUT2 genes. Recognizes and binds to the DNA sequence 5'-CGG-N(10)-CCG-3'.
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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PUT3 is a member of a family of at least 79 fungal transcription factors that contain a six-cysteine, two-zinc domain called a 'Zn2Cys6 binuclear cluster'. We have determined the crystal structure of the DNA binding region from the PUT3 protein bound to its cognate DNA target. The structure reveals that the PUT3 homodimer is bound asymmetrically to the DNA site. This asymmetry orients a beta-strand from one protein subunit into the minor groove of the DNA resulting in a partial amino acid-base pair intercalation and extensive direct and water-mediated protein interactions with the minor groove of the DNA. These interactions facilitate a sequence dependent kink at the centre of the DNA site and specify the intervening base pairs separating two DNA half-sites that are contacted in the DNA major groove. A comparison with the GAL4-DNA and PPR1-DNA complexes shows how a family of related DNA binding proteins can use a diverse set of mechanisms to discriminate between the base pairs separating conserved DNA half-sites.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/zm/1zme_consurf.spt"</scriptWhenChecked>
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1ZME is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZME OCA].
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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==Reference==
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</jmolCheckbox>
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Crystal structure of a PUT3-DNA complex reveals a novel mechanism for DNA recognition by a protein containing a Zn2Cys6 binuclear cluster., Swaminathan K, Flynn P, Reece RJ, Marmorstein R, Nat Struct Biol. 1997 Sep;4(9):751-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9303004 9303004]
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</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=1zme ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
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[[Category: Single protein]]
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[[Category: Marmorstein R]]
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[[Category: Marmorstein, R.]]
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[[Category: Swaminathan K]]
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[[Category: Swaminathan, K.]]
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[[Category: Binuclear cluster]]
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[[Category: Put3]]
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[[Category: Transcription factor]]
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[[Category: Zn2cys6]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 17:48:27 2008''
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Current revision

CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX

PDB ID 1zme

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