Crystal structure of the first eubacterial Mre11 nuclease reveals novel features that may discriminate substrates during DNA repair.
Mre11 nuclease plays a central role in the repair of cytotoxic and mutagenic DNA double-strand breaks. As X-ray structural information has been available only for the Pyrococcus furiosus enzyme (PfMre11), the conserved and variable features of this nuclease across the domains of life have not been experimentally defined. Our crystal structure and biochemical studies demonstrate that TM1635 from Thermotoga maritima, originally annotated as a putative nuclease, is an Mre11 endo/exonuclease (TmMre11) and the first such structure from eubacteria. TmMre11 and PfMre11 display similar overall structures, despite sequence identity in the twilight zone of only approximately 20%. However, they differ substantially in their DNA-specificity domains and in their dimeric organization. Residues in the nuclease domain are highly conserved, but those in the DNA-specificity domain are not. The structural differences likely affect how Mre11 from different organisms recognize and interact with single-stranded DNA, double-stranded DNA and DNA hairpin structures during DNA repair. The TmMre11 nuclease active site has no bound metal ions, but is conserved in sequence and structure with the exception of a histidine that is important in PfMre11 nuclease activity. Nevertheless, biochemical characterization confirms that TmMre11 possesses both endonuclease and exonuclease activities on single-stranded and double-stranded DNA substrates, respectively.
Das
Debanu
D
Joint Center for Structural Genomics, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
Moiani
Davide
D
Axelrod
Herbert L
HL
Miller
Mitchell D
MD
McMullan
Daniel
D
Jin
Kevin K
KK
Abdubek
Polat
P
Astakhova
Tamara
T
Burra
Prasad
P
Carlton
Dennis
D
Chiu
Hsiu-Ju
HJ
Clayton
Thomas
T
Deller
Marc C
MC
Duan
Lian
L
Ernst
Dustin
D
Feuerhelm
Julie
J
Grant
Joanna C
JC
Grzechnik
Anna
A
Grzechnik
Slawomir K
SK
Han
Gye Won
GW
Jaroszewski
Lukasz
L
Klock
Heath E
HE
Knuth
Mark W
MW
Kozbial
Piotr
P
Krishna
S Sri
SS
Kumar
Abhinav
A
Marciano
David
D
Morse
Andrew T
AT
Nigoghossian
Edward
E
Okach
Linda
L
Paulsen
Jessica
J
Reyes
Ron
R
Rife
Christopher L
CL
Sefcovic
Natasha
N
Tien
Henry J
HJ
Trame
Christine B
CB
van den Bedem
Henry
H
Weekes
Dana
D
Xu
Qingping
Q
Hodgson
Keith O
KO
Wooley
John
J
Elsliger
Marc-André
MA
Deacon
Ashley M
AM
Godzik
Adam
A
Lesley
Scott A
SA
Tainer
John A
JA
Wilson
Ian A
IA
D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000737:chemistry*; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004260:DNA Repair; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics; D004706:Endodeoxyribonucleases / Q000737:chemistry* / Q000235:genetics; D005090:Exodeoxyribonucleases / Q000737:chemistry* / Q000235:genetics; D008956:Models, Chemical; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D020124:Thermotoga maritima / Q000201:enzymology*
D001426:Bacterial Proteins; D004277:DNA, Single-Stranded; D004247:DNA; D004706:Endodeoxyribonucleases; D005090:Exodeoxyribonucleases