DNA photolyase N-terminal domain
DNA photolyase, N-terminal is an evolutionary conserved protein domain. This domain binds a light harvesting chromophore that enhanced the spectrum of photolyase or cryptochrome light absorption, i.e. an antenna.[1] It adopts the rossmann fold.[2]
| DNA photolyase, N-terminal | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | DNA_photolyase | ||||||||
| Pfam | PF00875 | ||||||||
| InterPro | IPR006050 | ||||||||
| PROSITE | PDOC00331 | ||||||||
| SCOP2 | 1qnf / SCOPe / SUPFAM | ||||||||
| |||||||||
| FeS-BCP | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Identifiers | |||||||||
| Symbol | DPRP | ||||||||
| Pfam | PF04244 | ||||||||
| InterPro | IPR007357 | ||||||||
| |||||||||
The cofactor may be either the pterin 5,10-Methenyltetrahydrofolate (MTHF, MHF) in folate photolyases (PDB: 4U63) or the deazaflavin 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF, FO1) in deazaflavin photolyases (PDB: 3CVV, 4CDN).[2] The 8-HDF ligand usually binds into this domain (next to the C-terminal half), while MHF tends to bind to an outside groove of this domain.[3] A structural signature for 8-HDF binding has been produced, highlighting amino acid residues that determine which antenna a photolyase can use.[4] Experiments on a Thermus thermophilus protein with this domain (P61497) shows that artificial substrates can be alternatively used for a modified absorption spectra. It naturally binds FMN in a pose similar to 8-HDF.[5] In addition, many cryptochromes, especially those from animals, bind no cofactors at this domain.[3]
Even though few eukaryotes (and no animals) can synthesize 8-HDF on their own,[6] many lineages nevertheless use deazaflavin photolyases. They probably receive 8-HDF from their endosymbiotic microbes.[4] Unlike many bacterial deazaflavin photolyases that accepts FMN as well as 8-HDF, one such enzyme from the fruit fly only accepts 8-HDF.[6]
The FeS-BCP N-terminal domain is homologous to this domain. Instead of an organic cofactor, its chromophore is an iron-sulphur cluster.[7]
References
- Tamada T, Kitadokoro K, Higuchi Y, Inaka K, Yasui A, de Ruiter PE, Eker AP, Miki K (November 1997). "Crystal structure of DNA photolyase from Anacystis nidulans". Nature Structural Biology. 4 (11): 887–91. doi:10.1038/nsb1197-887. PMID 9360600. S2CID 7041623.
- Sancar A (June 2003). "Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors". Chemical Reviews. 103 (6): 2203–37. doi:10.1021/cr0204348. PMID 12797829.
- Scheerer P, Zhang F, Kalms J, von Stetten D, Krauß N, Oberpichler I, Lamparter T (May 2015). "The class III cyclobutane pyrimidine dimer photolyase structure reveals a new antenna chromophore binding site and alternative photoreduction pathways". The Journal of Biological Chemistry. 290 (18): 11504–14. doi:10.1074/jbc.M115.637868. PMC 4416854. PMID 25784552.
- Kiontke S, Gnau P, Haselsberger R, Batschauer A, Essen LO (July 2014). "Structural and evolutionary aspects of antenna chromophore usage by class II photolyases". The Journal of Biological Chemistry. 289 (28): 19659–69. doi:10.1074/jbc.M113.542431. PMC 4094076. PMID 24849603.
- Klar T, Kaiser G, Hennecke U, Carell T, Batschauer A, Essen LO (November 2006). "Natural and non-natural antenna chromophores in the DNA photolyase from Thermus thermophilus". ChemBioChem. 7 (11): 1798–806. doi:10.1002/cbic.200600206. PMID 17051659. S2CID 44346656.
- Glas AF, Maul MJ, Cryle M, Barends TR, Schneider S, Kaya E, Schlichting I, Carell T (July 2009). "The archaeal cofactor F0 is a light-harvesting antenna chromophore in eukaryotes". Proceedings of the National Academy of Sciences of the United States of America. 106 (28): 11540–5. doi:10.1073/pnas.0812665106. PMC 2704855. PMID 19570997.
- Oberpichler I, Pierik AJ, Wesslowski J, Pokorny R, Rosen R, Vugman M, Zhang F, Neubauer O, Ron EZ, Batschauer A, Lamparter T (31 October 2011). "A photolyase-like protein from Agrobacterium tumefaciens with an iron-sulfur cluster". PLOS ONE. 6 (10): e26775. Bibcode:2011PLoSO...626775O. doi:10.1371/journal.pone.0026775. PMC 3204975. PMID 22066008.