| References |
|
|
Arita K,
Ariyoshi M,
Tochio H,
Nakamura Y and
Shirakawa M
(2008)
Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.
Nature
455:
818821.
|
|
|
Avvakumov GV,
Walker JR,
Xue S et al.
(2008)
Structural basis for recognition of hemi-methylated DNA by the SRA domain of human UHRF1.
Nature
455:
822825.
|
|
|
Barrett TE,
Savva R,
Panayotou G et al.
(1998)
Crystal structure of a G:T/U mismatch-specific DNA glycosylase: mismatch recognition by complementary-strand interactions.
Cell
92:
117129.
|
|
|
Cheng X and
Blumenthal RM
(1996)
Finding a basis for flipping bases.
Structure
4:
639645.
|
|
|
Daniels DS,
Woo TT,
Luu KX et al.
(2004)
DNA binding and nucleotide flipping by the human DNA repair protein AGT.
Nature Structural & Molecular Biology
11:
714720.
|
|
|
Duguid EM,
Rice PA and
He C
(2005)
The structure of the human AGT protein bound to DNA and its implications for damage detection.
Journal of Molecular Biology
350:
657666.
|
|
|
Fromme JC,
Banerjee A,
Huang SJ and
Verdine GL
(2004)
Structural basis for removal of adenine mispaired with 8-oxoguanine by MutY adenine DNA glycosylase.
Nature
427:
652656.
|
|
|
Goedecke K,
Pignot M,
Goody RS,
Scheidig AJ and
Weinhold E
(2001)
Structure of the N6-adenine DNA methyltransferase M.TaqI in complex with DNA and a cofactor analog.
Nature Structural Biology
8:
121125.
|
|
|
Hashimoto H,
Horton JR,
Zhang X et al.
(2008)
The SRA domain of UHRF1 flips 5-methylcytosine out of the DNA helix.
Nature
455:
826829.
|
|
|
Horton JR,
Liebert K,
Bekes M,
Jeltsch A and
Cheng X
(2006)
Structure and substrate recognition of the E. coli DNA adenine methyltransferase.
Journal of Molecular Biology
358:
559570.
|
|
|
Horton JR,
Liebert K,
Hattman S,
Jeltsch A and
Cheng X
(2005)
Transition from nonspecific to specific DNA interactions along the substrate-recognition pathway of dam methyltransferase.
Cell
121:
349361.
|
|
|
Horton JR,
Ratner G,
Banavali NK et al.
(2004)
Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase.
Nucleic Acids Research
32:
38773886.
|
|
|
Hosfield CM,
Guan Y,
Cunningham RP and
Tainer JA
(1999)
Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis.
Cell
98:
397408.
|
|
|
Klimasauskas S,
Kumar S,
Roberts RJ and
Cheng X
(1994)
HhaI methyltransferase flips its target base out of the DNA helix.
Cell
76:
357369.
|
|
|
Lariviere L and
Morera S
(2004)
Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase.
Journal of Biological Chemistry
279:
3471534720.
|
|
|
Lariviere L,
Sommer N and
Morera S
(2005)
Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.
Journal of Molecular Biology
352:
139150.
|
|
|
Lau AY,
Scharer OD,
Samson L,
Verdine GL and
Ellenberger T
(1998)
Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision.
Cell
95:
249258.
|
|
|
Lee TT,
Agarwalla S and
Stroud RM
(2005)
A unique RNA Fold in the RumA-RNA-cofactor ternary complex contributes to substrate selectivity and enzymatic function.
Cell
120:
599611.
|
|
|
Lukin M and
de Los Santos C
(2006)
NMR structures of damaged DNA.
Chemical Reviews
106:
607686.
|
|
|
Mees A,
Klar T,
Gnau P et al.
(2004)
Crystal structure of a photolyase bound to a CPD-like DNA lesion after in situ repair.
Science
306:
17891793.
|
|
|
Min JH and
Pavletich NP
(2007)
Recognition of DNA damage by the Rad4 nucleotide excision repair protein.
Nature
449:
570575.
|
|
|
O'Gara M,
Horton JR,
Roberts RJ and
Cheng X
(1998)
Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.
Nature Structural Biology
5:
872877.
|
|
|
Panayotou G,
Brown T,
Barlow T,
Pearl LH and
Savva R
(1998)
Direct measurement of the substrate preference of uracil-DNA glycosylase.
Journal of Biological Chemistry
273:
4550.
|
|
|
Parikh SS,
Mol CD,
Slupphaug G et al.
(1998)
Base excision repair initiation revealed by crystal structures and binding kinetics of human uracil-DNA glycosylase with DNA.
EMBO Journal
17:
52145226.
|
|
|
Parker JB,
Bianchet MA,
Krosky DJ et al.
(2007)
Enzymatic capture of an extrahelical thymine in the search for uracil in DNA.
Nature
449:
433437.
|
|
|
Reinisch KM,
Chen L,
Verdine GL and
Lipscomb WN
(1995)
The crystal structure of HaeIII methyltransferase convalently complexed to DNA: an extrahelical cytosine and rearranged base pairing.
Cell
82:
143153.
|
|
|
Roberts RJ
(1995)
On base flipping.
Cell
82:
912.
|
|
|
Schroeder LA,
Gries TJ,
Saecker RM et al.
(2009)
Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of E. coli RNA polymerase to promoter DNA.
Journal of Molecular Biology
385:
339349.
|
|
|
Scrima A,
Konickova R,
Czyzewski BK et al.
(2008)
Structural basis of UV DNA-damage recognition by the DDB1DDB2 complex.
Cell
135:
12131223.
|
|
|
Slupphaug G,
Mol CD,
Kavli B et al.
(1996)
A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA.
Nature
384:
8792.
|
|
|
Stivers JT,
Pankiewicz KW and
Watanabe KA
(1999)
Kinetic mechanism of damage site recognition and uracil flipping by E. coli uracil DNA glycosylase.
Biochemistry
38:
952963.
|
|
|
Tubbs JL,
Latypov V,
Kanugula S et al.
(2009)
Flipping of alkylated DNA damage bridges base and nucleotide excision repair.
Nature
459:
808813.
|
|
|
Vassylyev DG,
Kashiwagi T,
Mikami Y et al.
(1995)
Atomic model of a pyrimidine dimer excision repair enzyme complexed with a DNA substrate: structural basis for damaged DNA recognition.
Cell
83:
773782.
|
|
|
Werner RM,
Jiang YL,
Gordley RG et al.
(2000)
Stressing-out DNA? The contribution of serine-phosphodiester interactions in catalysis by uracil DNA glycosylase.
Biochemistry
39:
1258512594.
|
|
|
Yang CG,
Yi C,
Duguid EM et al.
(2008)
Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA.
Nature
452:
961965.
|
| Further Reading |
|
|
Bowman BR,
Lee S,
Wang S and
Verdine GL
(2008)
Structure of the E. coli DNA glycosylase AlkA bound to the ends of duplex DNA: a system for the structure determination of lesion-containing DNA.
Structure
16:
11661174.
|
|
|
Cheng X and
Blumenthal RM
(2008)
Mammalian DNA methyltransferases: a structural perspective.
Structure
16:
341350.
|
|
|
Klimasauskas S,
Szyperski T,
Serva S and
Wuthrich K
(1998)
Dynamic modes of the flipped-out cytosine during HhaI methyltransferase-DNA interactions in solution.
EMBO Journal
17:
317324.
|
|
|
Macbeth MR,
Schubert HL,
Vandemark AP et al.
(2005)
Inositol hexakisphosphate is bound in the ADAR2 core and required for RNA editing.
Science
309:
15341539.
|
|
|
Malone T,
Blumenthal RM and
Cheng X
(1995)
Structure-guided analysis reveals nine sequence motifs conserved among DNA amino-methyltransferases, and suggests a catalytic mechanism for these enzymes.
Journal of Molecular Biology
253:
618632.
|
|
|
Park HW,
Kim ST,
Sancar A and
Deisenhofer J
(1995)
Crystal structure of DNA photolyase from E. coli.
Science
268:
18661872.
|
|
|
Roberts RJ and
Cheng X
(1998)
Base flipping.
Annual Review of Biochemistry
67:
181198.
|
|
|
Schluckebier G,
O'Gara M,
Saenger W and
Cheng X
(1995)
Universal catalytic domain structure of AdoMet-dependent methyltransferases.
Journal of Molecular Biology
247:
1620.
|
|
|
Tubbs JL,
Pegg AE and
Tainer JA
(2007)
DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy.
DNA Repair (Amsterdam)
6:
11001115.
|
|
|
Yang CG,
Garcia K and
He C
(2009)
Damage detection and base flipping in direct DNA alkylation repair.
Chembiochem
10:
417423.
|