3umv

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<StructureSection load='3umv' size='340' side='right'caption='[[3umv]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
<StructureSection load='3umv' size='340' side='right'caption='[[3umv]], [[Resolution|resolution]] 1.71&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3umv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Japanese_rice Japanese rice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UMV FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3umv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Oryza_sativa_Japonica_Group Oryza sativa Japonica Group]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UMV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UMV FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=URE:UREA'>URE</scene></td></tr>
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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]] 1.705&#8491;</td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PHR, Os10g0167600, LOC_Os10g08580, OSJNAb0015J03.12 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=39947 Japanese rice])</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=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=URE:UREA'>URE</scene></td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Deoxyribodipyrimidine_photo-lyase Deoxyribodipyrimidine photo-lyase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.99.3 4.1.99.3] </span></td></tr>
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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=3umv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3umv OCA], [https://pdbe.org/3umv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3umv RCSB], [https://www.ebi.ac.uk/pdbsum/3umv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3umv ProSAT]</span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3umv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3umv OCA], [https://pdbe.org/3umv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3umv RCSB], [https://www.ebi.ac.uk/pdbsum/3umv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3umv ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[https://www.uniprot.org/uniprot/PHR_ORYSJ PHR_ORYSJ]] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutylpyrimidine dimers (CPDs), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation. Required for plant survival in the presence of UV-B light. Not involved in the repair of (6-4) photoproducts.<ref>PMID:12764611</ref> <ref>PMID:15965242</ref> <ref>PMID:17895582</ref> <ref>PMID:17397507</ref> <ref>PMID:18235036</ref> <ref>PMID:20227927</ref>
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[https://www.uniprot.org/uniprot/PHR_ORYSJ PHR_ORYSJ] Involved in repair of UV radiation-induced DNA damage. Catalyzes the light-dependent monomerization (300-600 nm) of cyclobutylpyrimidine dimers (CPDs), which are formed between adjacent bases on the same DNA strand upon exposure to ultraviolet radiation. Required for plant survival in the presence of UV-B light. Not involved in the repair of (6-4) photoproducts.<ref>PMID:12764611</ref> <ref>PMID:15965242</ref> <ref>PMID:17895582</ref> <ref>PMID:17397507</ref> <ref>PMID:18235036</ref> <ref>PMID:20227927</ref>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Ozone depletion increases terrestrial solar ultraviolet B (UV-B; 280-315 nm) radiation, intensifying the risks plants face from DNA damage, especially covalent cyclobutane pyrimidine dimers (CPD). Without efficient repair, UV-B destroys genetic integrity, but plant breeding creates rice cultivars with more robust photolyase (PHR) DNA repair activity as an environmental adaptation. So improved strains of Oryza sativa (rice), the staple food for Asia, have expanded rice cultivation worldwide. Efficient light-driven PHR enzymes restore normal pyrimidines to UV-damaged DNA by using blue light via flavin adenine dinucleotide to break pyrimidine dimers. Eukaryotes duplicated the photolyase gene, producing PHRs that gained functions and adopted activities that are distinct from those of prokaryotic PHRs yet are incompletely understood. Many multicellular organisms have two types of PHR: (6-4) PHR, which structurally resembles bacterial CPD PHRs but recognizes different substrates, and Class II CPD PHR, which is remarkably dissimilar in sequence from bacterial PHRs despite their common substrate. To understand the enigmatic DNA repair mechanisms of PHRs in eukaryotic cells, we determined the first crystal structure of a eukaryotic Class II CPD PHR from the rice cultivar Sasanishiki. Our 1.7 A resolution PHR structure reveals structure-activity relationships in Class II PHRs and tuning for enhanced UV tolerance in plants. Structural comparisons with prokaryotic Class I CPD PHRs identified differences in the binding site for UV-damaged DNA substrate. Convergent evolution of both flavin hydrogen bonding and a Trp electron transfer pathway establish these as critical functional features for PHRs. These results provide a paradigm for light-dependent DNA repair in higher organisms.
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Eukaryotic Class II Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals Basis for Improved Ultraviolet Tolerance in Plants.,Hitomi K, Arvai AS, Yamamoto J, Hitomi C, Teranishi M, Hirouchi T, Yamamoto K, Iwai S, Tainer JA, Hidema J, Getzoff ED J Biol Chem. 2012 Apr 6;287(15):12060-9. Epub 2011 Dec 14. PMID:22170053<ref>PMID:22170053</ref>
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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 3umv" style="background-color:#fffaf0;"></div>
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== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Deoxyribodipyrimidine photo-lyase]]
 
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[[Category: Japanese rice]]
 
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Arvai, A S]]
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[[Category: Oryza sativa Japonica Group]]
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[[Category: Getzoff, E D]]
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[[Category: Arvai AS]]
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[[Category: Hitomi, K]]
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[[Category: Getzoff ED]]
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[[Category: Tainer, J A]]
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[[Category: Hitomi K]]
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[[Category: Cpd cyclobutane pyrimidine dimer]]
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[[Category: Tainer JA]]
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[[Category: Dna repair]]
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[[Category: Flavoprotein]]
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[[Category: Lyase]]
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[[Category: Uv damaged dna]]
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Current revision

Eukaryotic Class II CPD photolyase structure reveals a basis for improved UV-tolerance in plants

PDB ID 3umv

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