1vas

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[[Image:1vas.gif|left|200px]]
 
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{{Structure
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==ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION==
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|PDB= 1vas |SIZE=350|CAPTION= <scene name='initialview01'>1vas</scene>, resolution 2.750&Aring;
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<StructureSection load='1vas' size='340' side='right'caption='[[1vas]], [[Resolution|resolution]] 2.75&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND=
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<table><tr><td colspan='2'>[[1vas]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_virus_T4 Escherichia virus T4]. The July 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Thymine Dimers'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_7 10.2210/rcsb_pdb/mom_2007_7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VAS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VAS 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]] 2.75&#8491;</td></tr>
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|GENE= DENV ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id= Bacteriophage T4])
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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=1vas FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vas OCA], [https://pdbe.org/1vas PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vas RCSB], [https://www.ebi.ac.uk/pdbsum/1vas PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vas ProSAT]</span></td></tr>
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}}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/END5_BPT4 END5_BPT4]
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== Evolutionary Conservation ==
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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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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/va/1vas_consurf.spt"</scriptWhenChecked>
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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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</jmolCheckbox>
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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=1vas ConSurf].
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<div style="clear:both"></div>
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'''ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION'''
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==See Also==
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*[[Endonuclease 3D structures|Endonuclease 3D structures]]
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__TOC__
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==Overview==
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</StructureSection>
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T4 endonuclease V is a DNA repair enzyme from bacteriophage T4 that catalyzes the first reaction step of the pyrimidine dimer-specific base excision repair pathway. The crystal structure of this enzyme complexed with a duplex DNA substrate, containing a thymine dimer, has been determined at 2.75 A resolution. The atomic structure of the complex reveals the unique conformation of the DNA duplex, which exhibits a sharp kink with a 60 degree inclination at the central thymine dimer. The adenine base complementary to the 5' side of the thymine dimer is completely flipped out of the DNA duplex and trapped in a cavity on the protein surface. These structural features allow an understanding of the catalytic mechanism and implicate a general mechanism of how other repair enzymes recognize damaged DNA duplexes.
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[[Category: Escherichia virus T4]]
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[[Category: Large Structures]]
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==About this Structure==
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[[Category: RCSB PDB Molecule of the Month]]
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1VAS is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteriophage_t4 Bacteriophage t4]. The following page contains interesting information on the relation of 1VAS with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb91_1.html Thymine Dimers]]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VAS OCA].
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==Reference==
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Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition., Vassylyev DG, Kashiwagi T, Mikami Y, Ariyoshi M, Iwai S, Ohtsuka E, Morikawa K, Cell. 1995 Dec 1;83(5):773-82. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8521494 8521494]
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[[Category: Bacteriophage t4]]
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[[Category: Single protein]]
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[[Category: Thymine Dimers]]
[[Category: Thymine Dimers]]
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[[Category: Ariyoshi, M.]]
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[[Category: Ariyoshi M]]
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[[Category: Iwai, S.]]
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[[Category: Iwai S]]
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[[Category: Kashiwagi, T.]]
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[[Category: Kashiwagi T]]
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[[Category: Mikami, Y.]]
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[[Category: Mikami Y]]
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[[Category: Morikawa, K.]]
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[[Category: Morikawa K]]
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[[Category: Ohtsuka, E.]]
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[[Category: Ohtsuka E]]
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[[Category: Vassylyev, D G.]]
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[[Category: Vassylyev DG]]
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[[Category: double helix]]
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[[Category: protein-dna complex]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:43:03 2008''
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Current revision

ATOMIC MODEL OF A PYRIMIDINE DIMER SPECIFIC EXCISION REPAIR ENZYME COMPLEXED WITH A DNA SUBSTRATE: STRUCTURAL BASIS FOR DAMAGED DNA RECOGNITION

PDB ID 1vas

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