Flipping of alkylated DNA damage bridges base and nucleotide excision repair.
Alkyltransferase-like proteins (ATLs) share functional motifs with the cancer chemotherapy target O(6)-alkylguanine-DNA alkyltransferase (AGT) and paradoxically protect cells from the biological effects of DNA alkylation damage, despite lacking the reactive cysteine and alkyltransferase activity of AGT. Here we determine Schizosaccharomyces pombe ATL structures without and with damaged DNA containing the endogenous lesion O(6)-methylguanine or cigarette-smoke-derived O(6)-4-(3-pyridyl)-4-oxobutylguanine. These results reveal non-enzymatic DNA nucleotide flipping plus increased DNA distortion and binding pocket size compared to AGT. Our analysis of lesion-binding site conservation identifies new ATLs in sea anemone and ancestral archaea, indicating that ATL interactions are ancestral to present-day repair pathways in all domains of life. Genetic connections to mammalian XPG (also known as ERCC5) and ERCC1 in S. pombe homologues Rad13 and Swi10 and biochemical interactions with Escherichia coli UvrA and UvrC combined with structural results reveal that ATLs sculpt alkylated DNA to create a genetic and structural intersection of base damage processing with nucleotide excision repair.
Tubbs
Julie L
JL
Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, California 92037, USA.
Latypov
Vitaly
V
Kanugula
Sreenivas
S
Butt
Amna
A
Melikishvili
Manana
M
Kraehenbuehl
Rolf
R
Fleck
Oliver
O
Marriott
Andrew
A
Watson
Amanda J
AJ
Verbeek
Barbara
B
McGown
Gail
G
Thorncroft
Mary
M
Santibanez-Koref
Mauro F
MF
Millington
Christopher
C
Arvai
Andrew S
AS
Kroeger
Matthew D
MD
Peterson
Lisa A
LA
Williams
David M
DM
Fried
Michael G
MG
Margison
Geoffrey P
GP
Pegg
Anthony E
AE
Tainer
John A
JA
D019883:Alkyl and Aryl Transferases / Q000737:chemistry* / Q000378:metabolism*; D000478:Alkylation; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004249:DNA Damage; D004260:DNA Repair; D006147:Guanine / Q000031:analogs & derivatives / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008958:Models, Molecular; D011485:Protein Binding; D011487:Protein Conformation
C473029:O(6)-(4-oxo-4-(3-pyridyl)butyl)guanine; D006147:Guanine; D004247:DNA; C008449:O-(6)-methylguanine; C510506:ATL1 protein, S pombe; D019883:Alkyl and Aryl Transferases