1dnp

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(New page: 200px<br /><applet load="1dnp" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dnp, resolution 2.3&Aring;" /> '''STRUCTURE OF DEOXYRIB...)
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[[Image:1dnp.jpg|left|200px]]<br /><applet load="1dnp" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1dnp, resolution 2.3&Aring;" />
 
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'''STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE'''<br />
 
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==Overview==
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==STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE==
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Photolyase repairs ultraviolet (UV) damage to DNA by splitting the, cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane, pyrimidine dimer (Pyr &lt;&gt; Pyr). The reaction is initiated by blue light and, proceeds through long-range energy transfer, single electron transfer, and, enzyme catalysis by a radical mechanism. The three-dimensional, crystallographic structure of DNA photolyase from Escherichia coli is, presented and the atomic model was refined to an R value of 0.172 at 2.3 A, resolution. The polypeptide chain of 471 amino acids is folded into an, amino-terminal alpha/beta domain resembling dinucleotide binding domains, and a carboxyl-terminal helical domain; a loop of 72 residues connects the, domains. The light-harvesting cofactor, 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between, the two domains. Energy transfer from MTHF to the catalytic cofactor, flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 A. The, FAD adopts a U-shaped conformation between two helix clusters in the, center of the helical domain and is accessible through a hole in the, surface of this domain. Dimensions and polarity of the hole match those of, a Pyr &lt;&gt; Pyr dinucleotide, suggesting that the Pyr &lt;&gt; Pyr "flips out" of, the helix to fit into this hole, and that electron transfer between the, flavin and the Pyr &lt;&gt; Pyr occurs over van der Waals contact distance.
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<StructureSection load='1dnp' size='340' side='right'caption='[[1dnp]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1dnp]] 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=1DNP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DNP FirstGlance]. <br>
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1DNP is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli] with FAD and MHF as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DNP OCA].
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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]] 2.3&#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=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MHF:5,10-METHENYL-6,7,8-TRIHYDROFOLIC+ACID'>MHF</scene></td></tr>
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==Reference==
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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=1dnp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dnp OCA], [https://pdbe.org/1dnp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dnp RCSB], [https://www.ebi.ac.uk/pdbsum/1dnp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dnp ProSAT]</span></td></tr>
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Crystal structure of DNA photolyase from Escherichia coli., Park HW, Kim ST, Sancar A, Deisenhofer J, Science. 1995 Jun 30;268(5219):1866-72. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7604260 7604260]
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</table>
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[[Category: Deoxyribodipyrimidine photo-lyase]]
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== Function ==
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[https://www.uniprot.org/uniprot/PHR_ECOLI PHR_ECOLI] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutyl pyrimidine dimers (in cis-syn configuration), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation.
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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/dn/1dnp_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=1dnp ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Escherichia coli]]
[[Category: Escherichia coli]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Deisenhofer, J.]]
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[[Category: Deisenhofer J]]
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[[Category: Park, H.W.]]
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[[Category: Park H-W]]
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[[Category: Sancar, A.]]
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[[Category: Sancar A]]
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[[Category: FAD]]
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[[Category: MHF]]
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[[Category: carbon-carbon]]
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[[Category: dna repair]]
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[[Category: electron transfer]]
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[[Category: excitation energy transfer]]
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[[Category: lyase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 13:25:50 2007''
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Current revision

STRUCTURE OF DEOXYRIBODIPYRIMIDINE PHOTOLYASE

PDB ID 1dnp

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