Photolyase
Cryptochrome/photolyase, C-terminal, FAD binding | |||||||||||
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deoxyribodipyrimidine photo-lyase (CPD) | |||||||||
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ExPASy NiceZyme view | | ||||||||
KEGG | KEGG entry | ||||||||
MetaCyc | metabolic pathway | ||||||||
PRIAM | profile | ||||||||
PDB structures | RCSB PDB PDBe PDBsum | ||||||||
Gene Ontology | AmiGO / QuickGO | ||||||||
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Photolyases (
Function
Photolyases bind complementary DNA strands and break certain types of pyrimidine dimers that arise when a pair of thymine or cytosine bases on the same strand of DNA become covalently linked. The bond length of this dimerization is shorter than the bond length of normal B-DNA structure which produces an incorrect template for replication and transcription.[7] The more common covalent linkage involves the formation of a cyclobutane bridge. Photolyases have a high affinity for these lesions and reversibly bind and convert them back to the original bases. The photolyase-catalyzed DNA repair process by which cyclobutane pyrimidine dimers are resolved has been studied by time-resolved crystallography and computational analysis to allow atomic visualization of the process.[8]
Evolution
Photolyase is a
Photolyases are
On the basis of sequence similarities DNA photolyases can be grouped into a few classes:[14][15]
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- Class 1 CPD photolyases are enzymes that process cyclobutane pyrimidine dimer (CPD) lesions from Gram-negative and Gram-positive bacteria, as well as the halophilic Halobacterium halobium.[16]
- Class 2 CPD photolyases also process CPD lesions. They are found in plants like the thale cress Arabidopsis thaliana and the rice.
- The plant and fungi cryptochromes are similar to Class 1 CPDs. They are blue light photoreceptors that mediate blue light-induced gene expression and modulation of circadian rhythms.
- Class 3 CPD lyases make up a sister group to the plant cryptochromes, which in turn are a sister group to class 1 CPDs.
- The Cry-DASH group are CPD lyases highly specific for single-stranded DNA. Members include Xenopus laevis, and AtCry3 from Arabidopsis thaliana.[10] DASH was initially named after Drosophila, Arabidopsis, Synechocystis, and Human, four taxa initially thought to carry this family of lyases. The categorization has since changed. The "Cry" part of their name was due to initial assumptions that they were cryptochromes.[14]
- Eukaryotic (6-4)DNA photolyases form a group with animal cryptochromes that control circadian rhythms. They are found in diverse species including Drosophila and humans. The cryptochromes have their own detailed grouping.[15]
- Bacterial 6-4 lyases (InterPro: IPR007357), also known as the FeS-BCP group, form their own outgroup relative to all photolyases.
The non-class 2 branch of CPDs tend to be grouped into class 1 in some systems such as PRINTS (PR00147). Although the members of the smaller groups are agreed upon, the phylogeny can vary greatly among authors due to differences in methodology, leading to some confusion with authors who try to fit everything (sparing FeS-BCP) into a two-class classification.
Application
Adding photolyase from a
Human proteins containing this domain
Cryptochromes:
Nomenclature
The systematic name of this enzyme class is deoxyribocyclobutadipyrimidine pyrimidine-lyase. Other names in common use include photoreactivating enzyme, DNA photolyase, DNA-photoreactivating enzyme, DNA cyclobutane dipyrimidine photolyase, DNA photolyase, deoxyribonucleic photolyase, deoxyribodipyrimidine photolyase, photolyase, PRE, PhrB photolyase, deoxyribonucleic cyclobutane dipyrimidine photolyase, phr A photolyase, dipyrimidine photolyase (photosensitive), and deoxyribonucleate pyrimidine dimer lyase (photosensitive). This enzyme belongs to the family of lyases, specifically in the "catch-all" class of carbon-carbon lyases.
References
- PMID 28880077.
- PMID 21606324.
- ^ Kelner, A. 1949 Effect of visible light on the recovery of Streptomyces griseus conidia from ultra-violet irradiation injury. Proc. Natl. Acad. Sci. U. S., 35, 73-79
- ^ Dulbecco R. Reactivation of ultra-violet-inactivated bacteriophage by visible light. Nature. 1949 Jun 18;163(4155):949. doi: 10.1038/163949b0. PMID 18229246
- ^ Dulbecco R. Experiments on photoreactivation of bacteriophages inactivated with ultraviolet radiation. J Bacteriol. 1950 Mar;59(3):329-47. doi: 10.1128/jb.59.3.329-347.1950. PMID 15436402; PMCID: PMC385765
- ^ Friedberg EC. A history of the DNA repair and mutagenesis field: I. The discovery of enzymatic photoreactivation. DNA Repair (Amst). 2015 Sep;33:35-42. doi: 10.1016/j.dnarep.2015.06.007. Epub 2015 Jun 24. PMID 26151545
- OCLC 984382855.
- ^ Maestre-Reyna M, Wang PH, Nango E, Hosokawa Y, Saft M, Furrer A, Yang CH, Gusti Ngurah Putu EP, Wu WJ, Emmerich HJ, Caramello N, Franz-Badur S, Yang C, Engilberge S, Wranik M, Glover HL, Weinert T, Wu HY, Lee CC, Huang WC, Huang KF, Chang YK, Liao JH, Weng JH, Gad W, Chang CW, Pang AH, Yang KC, Lin WT, Chang YC, Gashi D, Beale E, Ozerov D, Nass K, Knopp G, Johnson PJM, Cirelli C, Milne C, Bacellar C, Sugahara M, Owada S, Joti Y, Yamashita A, Tanaka R, Tanaka T, Luo F, Tono K, Zarzycka W, Müller P, Alahmad MA, Bezold F, Fuchs V, Gnau P, Kiontke S, Korf L, Reithofer V, Rosner CJ, Seiler EM, Watad M, Werel L, Spadaccini R, Yamamoto J, Iwata S, Zhong D, Standfuss J, Royant A, Bessho Y, Essen LO, Tsai MD. Visualizing the DNA repair process by a photolyase at atomic resolution. Science. 2023 Dec;382(6674):eadd7795. doi: 10.1126/science.add7795. Epub 2023 Dec 1. PMID 38033054
- PMID 18235036.)
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: CS1 maint: multiple names: authors list (link - ^ PMID 17062752.
- PMID 19228922.
- ^ Jaikumar NS, Dorn KM, Baas D, Wilke B, Kapp C, Snapp SS. Nucleic acid damage and DNA repair are affected by freezing stress in annual wheat (Triticum aestivum) and by plant age and freezing in its perennial relative (Thinopyrum intermedium). Am J Bot. 2020 Dec;107(12):1693-1709. doi: 10.1002/ajb2.1584. Epub 2020 Dec 19. PMID 33340368
- PMID 12797829.
- ^ PMID 25784552.
- ^ PMID 22442365.
- ^ McCready S, Marcello L. Repair of UV damage in Halobacterium salinarum. Biochem Soc Trans. 2003 Jun;31(Pt 3):694-8. doi: 10.1042/bst0310694. PMID 12773185
- PMID 10393932.
Further reading
- Eker AP, Fichtinger-Schepman AM (1975). "Studies on a DNA photoreactivating enzyme from Streptomyces griseus II. Purification of the enzyme". Biochim. Biophys. Acta. 378 (1): 54–63. PMID 804322.
- Sancar GB, Smith FW, Reid R, Payne G, Levy M, Sancar A (1987). "Action mechanism of Escherichia coli DNA photolyase. I. Formation of the enzyme-substrate complex". J. Biol. Chem. 262 (1): 478–85. PMID 3539939.
- Setlow JK, Bollum FJ (1968). "The minimum size of the substrate for yeast photoreactivating enzyme". Biochim. Biophys. Acta. 157 (2): 233–7. PMID 5649902.
External links
- Media related to Photolyase at Wikimedia Commons