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Noncognate DNA damage prevents the formation of the active conformation of the Y‐family DNA polymerases DinB and DNA polymerase κ
Author(s) -
Nevin Philip,
Lu Xueguang,
Zhang Ke,
Engen John R.,
Beuning Penny J.
Publication year - 2015
Publication title -
the febs journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 204
eISSN - 1742-4658
pISSN - 1742-464X
DOI - 10.1111/febs.13304
Subject(s) - dna polymerase , dna clamp , dna polymerase ii , polymerase , dna polymerase i , biology , dna polymerase mu , dna , dna replication , primase , dna polymerase delta , biochemistry , genetics , microbiology and biotechnology , circular bacterial chromosome , reverse transcriptase , polymerase chain reaction , gene
Y‐family DNA polymerases are specialized to copy damaged DNA , and are associated with increased mutagenesis, owing to their low fidelity. It is believed that the mechanism of nucleotide selection by Y‐family DNA polymerases involves conformational changes preceding nucleotidyl transfer, but there is limited experimental evidence for such structural changes. In particular, nucleotide‐induced conformational changes in bacterial or eukaryotic Y‐family DNA polymerases have, to date, not been extensively characterized. Using hydrogen–deuterium exchange mass spectrometry, we demonstrate here that the Escherichia coli Y‐family DNA polymerase DinB and its human ortholog DNA polymerase κ undergo a conserved nucleotide‐induced conformational change in the presence of undamaged DNA and the correct incoming nucleotide. Notably, this holds true for damaged DNA containing N 2 ‐furfuryl‐deoxyguanosine, which is efficiently copied by these two polymerases, but not for damaged DNA containing the major groove modification O 6 ‐methyl‐deoxyguanosine, which is a poor substrate. Our observations suggest that DinB and DNA polymerase κ utilize a common mechanism for nucleotide selection involving a conserved prechemical conformational transition promoted by the correct nucleotide and only preferred DNA substrates.