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2e0i

From Proteopedia

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[[Image:2e0i.gif|left|200px]]
 
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{{Structure
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==Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor==
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|PDB= 2e0i |SIZE=350|CAPTION= <scene name='initialview01'>2e0i</scene>, resolution 2.80&Aring;
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<StructureSection load='2e0i' size='340' side='right'caption='[[2e0i]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>
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<table><tr><td colspan='2'>[[2e0i]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Sulfurisphaera_tokodaii_str._7 Sulfurisphaera tokodaii str. 7]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E0I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E0I FirstGlance]. <br>
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|ACTIVITY= <span class='plainlinks'>[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] </span>
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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]] 2.8&#8491;</td></tr>
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|GENE= ST0889 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=111955 Sulfolobus tokodaii])
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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=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</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=2e0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e0i OCA], [https://pdbe.org/2e0i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e0i RCSB], [https://www.ebi.ac.uk/pdbsum/2e0i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e0i 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=2e0i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e0i OCA], [http://www.ebi.ac.uk/pdbsum/2e0i PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2e0i RCSB]</span>
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== Function ==
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}}
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[https://www.uniprot.org/uniprot/F9VNB1_SULTO F9VNB1_SULTO]
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== Evolutionary Conservation ==
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'''Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor'''
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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/e0/2e0i_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=2e0i ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
UV exposure of DNA molecules induces serious DNA lesions. The cyclobutane pyrimidine dimer (CPD) photolyase repairs CPD-type - lesions by using the energy of visible light. Two chromophores for different roles have been found in this enzyme family; one catalyzes the CPD repair reaction and the other works as an antenna pigment that harvests photon energy. The catalytic cofactor of all known photolyases is FAD, whereas several light-harvesting cofactors are found. Currently, 5,10-methenyltetrahydrofolate (MTHF), 8-hydroxy-5-deaza-riboflavin (8-HDF) and FMN are the known light-harvesting cofactors, and some photolyases lack the chromophore. Three crystal structures of photolyases from Escherichia coli (Ec-photolyase), Anacystis nidulans (An-photolyase), and Thermus thermophilus (Tt-photolyase) have been determined; however, no archaeal photolyase structure is available. A similarity search of archaeal genomic data indicated the presence of a homologous gene, ST0889, on Sulfolobus tokodaii strain7. An enzymatic assay reveals that ST0889 encodes photolyase from S. tokodaii (St-photolyase). We have determined the crystal structure of the St-photolyase protein to confirm its structural features and to investigate the mechanism of the archaeal DNA repair system with light energy. The crystal structure of the St-photolyase is superimposed very well on the three known photolyases including the catalytic cofactor FAD. Surprisingly, another FAD molecule is found at the position of the light-harvesting cofactor. This second FAD molecule is well accommodated in the crystal structure, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase.
UV exposure of DNA molecules induces serious DNA lesions. The cyclobutane pyrimidine dimer (CPD) photolyase repairs CPD-type - lesions by using the energy of visible light. Two chromophores for different roles have been found in this enzyme family; one catalyzes the CPD repair reaction and the other works as an antenna pigment that harvests photon energy. The catalytic cofactor of all known photolyases is FAD, whereas several light-harvesting cofactors are found. Currently, 5,10-methenyltetrahydrofolate (MTHF), 8-hydroxy-5-deaza-riboflavin (8-HDF) and FMN are the known light-harvesting cofactors, and some photolyases lack the chromophore. Three crystal structures of photolyases from Escherichia coli (Ec-photolyase), Anacystis nidulans (An-photolyase), and Thermus thermophilus (Tt-photolyase) have been determined; however, no archaeal photolyase structure is available. A similarity search of archaeal genomic data indicated the presence of a homologous gene, ST0889, on Sulfolobus tokodaii strain7. An enzymatic assay reveals that ST0889 encodes photolyase from S. tokodaii (St-photolyase). We have determined the crystal structure of the St-photolyase protein to confirm its structural features and to investigate the mechanism of the archaeal DNA repair system with light energy. The crystal structure of the St-photolyase is superimposed very well on the three known photolyases including the catalytic cofactor FAD. Surprisingly, another FAD molecule is found at the position of the light-harvesting cofactor. This second FAD molecule is well accommodated in the crystal structure, suggesting that FAD works as a novel light-harvesting cofactor of photolyase. In addition, two of the four CPD recognition residues in the crystal structure of An-photolyase are not found in St-photolyase, which might utilize a different mechanism to recognize the CPD from that of An-photolyase.
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==About this Structure==
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Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor.,Fujihashi M, Numoto N, Kobayashi Y, Mizushima A, Tsujimura M, Nakamura A, Kawarabayasi Y, Miki K J Mol Biol. 2007 Jan 26;365(4):903-10. Epub 2006 Oct 7. PMID:17107688<ref>PMID:17107688</ref>
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2E0I is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Sulfolobus_tokodaii Sulfolobus tokodaii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E0I OCA].
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==Reference==
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Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: implication of a novel light-harvesting cofactor., Fujihashi M, Numoto N, Kobayashi Y, Mizushima A, Tsujimura M, Nakamura A, Kawarabayasi Y, Miki K, J Mol Biol. 2007 Jan 26;365(4):903-10. Epub 2006 Oct 7. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17107688 17107688]
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[[Category: Deoxyribodipyrimidine photo-lyase]]
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[[Category: Single protein]]
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[[Category: Sulfolobus tokodaii]]
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[[Category: Fujihashi, M.]]
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[[Category: Kawarabayashi, Y.]]
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[[Category: Kobayashi, Y.]]
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[[Category: Miki, K.]]
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[[Category: Mizushima, A.]]
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[[Category: Nakamura, A.]]
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[[Category: Numoto, N.]]
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[[Category: Tsujimura, M.]]
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[[Category: crystal structure]]
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[[Category: dna repair]]
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[[Category: fad]]
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[[Category: photolyase]]
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[[Category: sulfolobus tokodaii]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:41:55 2008''
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2e0i" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Sulfurisphaera tokodaii str. 7]]
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[[Category: Fujihashi M]]
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[[Category: Kawarabayashi Y]]
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[[Category: Kobayashi Y]]
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[[Category: Miki K]]
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[[Category: Mizushima A]]
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[[Category: Nakamura A]]
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[[Category: Numoto N]]
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[[Category: Tsujimura M]]

Current revision

Crystal structure of archaeal photolyase from Sulfolobus tokodaii with two FAD molecules: Implication of a novel light-harvesting cofactor

PDB ID 2e0i

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