title: Chemical synthesis, crystal structure and enzymatic evaluation of a dinucleotide spore photoproduct analogue containing a formacetal linker.
abstract: Spore photoproduct (SP) is the exclusive DNA photodamage product found in bacterial endospores. Its photoformation and repair by a metalloenzyme spore photoproduct lyase (SPL) composes the unique SP biochemistry. Despite the fact that the SP was discovered almost 50 years ago, its crystal structure is still unknown and the lack of structural information greatly hinders the study of SP biochemistry. Employing a formacetal linker and organic synthesis, we successfully prepared a dinucleotide SP isostere 5R-CH(2) SP, which contains a neutral CH(2) moiety between the two thymine residues instead of a phosphate. The neutral linker dramatically facilitates the crystallization process, allowing us to obtain the crystal structure for this intriguing thymine dimer half a century after its discovery. Further ROESY spectroscopic, DFT computational, and enzymatic studies of this 5R-CH(2) SP compound prove that it possesses similar properties with the 5R-SP species, suggesting that the revealed structure truly reflects that of SP generated in Nature.
authors.affiliation: Department of Chemistry and Chemical Biology, Indiana University, Purdue University Indianapolis (IUPUI), Indianapolis, IN 46202, USA.
authors.forename: Gengjie
authors.initials: G
authors.lastname: Lin
authors.forename: Chun-Hsing
authors.initials: CH
authors.lastname: Chen
authors.forename: Maren
authors.initials: M
authors.lastname: Pink
authors.forename: Jingzhi
authors.initials: J
authors.lastname: Pu
authors.forename: Lei
authors.initials: L
authors.lastname: Li
mesh_terms: D001412:Bacillus subtilis / Q000737:chemistry* / Q000201:enzymology / Q000378:metabolism; D002384:Catalysis; D018360:Crystallography, X-Ray; D004249:DNA Damage; D004260:DNA Repair; D004269:DNA, Bacterial / Q000737:chemistry / Q000378:metabolism* / Q000528:radiation effects*; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry*; D055668:Photochemical Processes; D011506:Proteins; D011740:Pyrimidine Dimers / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013171:Spores, Bacterial / Q000235:genetics / Q000378:metabolism*; D013237:Stereoisomerism; D013941:Thymine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D014466:Ultraviolet Rays
chemical_list: D004269:DNA, Bacterial; D009841:Oligonucleotides; D011506:Proteins; D011740:Pyrimidine Dimers; C009484:5-thyminyl-5,6-dihydrothymine; C088014:spore photoproduct lyase; D013941:Thymine