| Structural highlights
3umv is a 2 chain structure with sequence from Japanese rice. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , |
| Gene: | PHR, Os10g0167600, LOC_Os10g08580, OSJNAb0015J03.12 (Japanese rice) |
| Activity: | Deoxyribodipyrimidine photo-lyase, with EC number 4.1.99.3 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Function
[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.[1] [2] [3] [4] [5] [6]
Publication Abstract from PubMed
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.
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[7]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Hirouchi T, Nakajima S, Najrana T, Tanaka M, Matsunaga T, Hidema J, Teranishi M, Fujino T, Kumagai T, Yamamoto K. A gene for a Class II DNA photolyase from Oryza sativa: cloning of the cDNA by dilution-amplification. Mol Genet Genomics. 2003 Jul;269(4):508-16. Epub 2003 May 22. PMID:12764611 doi:http://dx.doi.org/10.1007/s00438-003-0856-9
- ↑ Ueda T, Sato T, Hidema J, Hirouchi T, Yamamoto K, Kumagai T, Yano M. qUVR-10, a major quantitative trait locus for ultraviolet-B resistance in rice, encodes cyclobutane pyrimidine dimer photolyase. Genetics. 2005 Dec;171(4):1941-50. Epub 2005 Jun 18. PMID:15965242 doi:http://dx.doi.org/10.1534/genetics.105.044735
- ↑ Yamamoto A, Hirouchi T, Mori T, Teranishi M, Hidema J, Morioka H, Kumagai T, Yamamoto K. Biochemical and biological properties of DNA photolyases derived from utraviolet-sensitive rice cultivars. Genes Genet Syst. 2007 Aug;82(4):311-9. PMID:17895582
- ↑ Hidema J, Taguchi T, Ono T, Teranishi M, Yamamoto K, Kumagai T. Increase in CPD photolyase activity functions effectively to prevent growth inhibition caused by UVB radiation. Plant J. 2007 Apr;50(1):70-9. PMID:17397507 doi:http://dx.doi.org/10.1111/j.1365-313X.2007.03041.x
- ↑ Teranishi M, Nakamura K, Morioka H, Yamamoto K, Hidema J. The native cyclobutane pyrimidine dimer photolyase of rice is phosphorylated. Plant Physiol. 2008 Apr;146(4):1941-51. doi: 10.1104/pp.107.110189. Epub 2008 Jan, 30. PMID:18235036 doi:http://dx.doi.org/10.1104/pp.107.110189
- ↑ Okafuji A, Biskup T, Hitomi K, Getzoff ED, Kaiser G, Batschauer A, Bacher A, Hidema J, Teranishi M, Yamamoto K, Schleicher E, Weber S. Light-induced activation of class II cyclobutane pyrimidine dimer photolyases. DNA Repair (Amst). 2010 May 4;9(5):495-505. doi: 10.1016/j.dnarep.2010.01.014., Epub 2010 Mar 15. PMID:20227927 doi:http://dx.doi.org/10.1016/j.dnarep.2010.01.014
- ↑ Hitomi K, Arvai AS, Yamamoto J, Hitomi C, Teranishi M, Hirouchi T, Yamamoto K, Iwai S, Tainer JA, Hidema J, Getzoff ED. Eukaryotic Class II Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals Basis for Improved Ultraviolet Tolerance in Plants. J Biol Chem. 2012 Apr 6;287(15):12060-9. Epub 2011 Dec 14. PMID:22170053 doi:10.1074/jbc.M111.244020
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