1zme

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[[Image:1zme.gif|left|200px]]
 
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{{Structure
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==CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX==
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|PDB= 1zme |SIZE=350|CAPTION= <scene name='initialview01'>1zme</scene>, resolution 2.5&Aring;
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<StructureSection load='1zme' size='340' side='right'caption='[[1zme]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=5IU:5-IODO-2&#39;-DEOXYURIDINE-5&#39;-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
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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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|ACTIVITY=
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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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|GENE=
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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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|DOMAIN=
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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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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zme FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zme OCA], [http://www.ebi.ac.uk/pdbsum/1zme PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zme RCSB]</span>
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== Function ==
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}}
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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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'''CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX'''
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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==Overview==
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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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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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<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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==About this Structure==
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</jmolCheckbox>
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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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</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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==Reference==
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__TOC__
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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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</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: complex (transcription regulation/dna)]]
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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 Mon Mar 31 01:38:43 2008''
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Current revision

CRYSTAL STRUCTURE OF PUT3/DNA COMPLEX

PDB ID 1zme

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