The complex structures of ALKBH2 mutants cross-linked to dsDNA reveal the conformational swing of β-hairpin

Science China Chemistry

Volumn 57, Issue 2, 2014, Pages 307-313

  Chen, Baoen ^a   Gan, Jianhua ^b   Yang, Caiguang ^a  

^a SHANGHAI INSTITUTE OF MATERIA MEDICA   (China)

^b FUDAN UNIVERSITY   (China)

Author keywords

hairpin motif; ALKBH2; chemical cross linking; damage detection; DNA repair

Indexed keywords

ALKBH2; BASE FLIPPING; CHEMICAL CROSS-LINKING; COMPLEX STRUCTURE; DNA REPAIR; DOUBLE STRANDED DNA; LOCAL REGION; MAMMALIAN ALKB HOMOLOGUES;

CONFORMATIONS; CROSSLINKING; DAMAGE DETECTION; MAMMALS;

DNA;

EID: 84893843492     PISSN: 16747291     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11426-013-5029-z     Document Type: Article

References (29)

1. Sedgwick B. Repairing DNA-methylation damage. Nat Rev Mol Cell Biol, 2004, 5(2): 148-157 (Pubitemid 38160257)
2. Lindahl T, Sedgwick B, Sekiguchi M, Nakabeppu Y. Regulation and expression of the adaptive response to alkylating agents. Annu Rev Biochem, 1988, 57: 133-157
3. Sedgwick B, Bates PA, Paik J, Jacobs SC, Lindahl T. Repair of alkylated DNA: Recent advances. DNA Repair (Amst), 2007, 6(4): 429-442 (Pubitemid 46357047)
4. Mishina Y, Duguid EM, He C. Direct reversal of DNA alkylation damage. Chem Rev, 2006, 106(2): 215-232 (Pubitemid 43322986)
5. Falnes PO, Johansen RF, Seeberg E. AlkB-mediated oxidative demethylation reverses DNA damage in Escherichia coli. Nature, 2002, 419(6903): 178-182 (Pubitemid 35025447)
6. Aas PA, Otterlei M, Falnes PO, Vagbo CB, Skorpen F, Akbari M, Sundheim O, Bjoras M, Slupphaug G, Seeberg E, Krokan HE. Human and bacterial oxidative demethylases repair alkylation damage in both RNA and DNA. Nature, 2003, 421(6925): 859-863 (Pubitemid 36258356)
7. Duncan T, Trewick SC, Koivisto P, Bates PA, Lindahl T, Sedgwick B. Reversal of DNA alkylation damage by two human dioxygenases. Proc Natl Acad Sci USA, 2002, 99(26): 16660-16665 (Pubitemid 36034029)
8. Ringvoll J, Nordstrand LM, Vagbo CB, Talstad V, Reite K, Aas PA, Lauritzen KH, Liabakk NB, Bjork A, Doughty RW, Falnes PO, Krokan HE, Klungland A. Repair deficient mice reveal mABH2 as the primary oxidative demethylase for repairing 1meA and 3meC lesions in DNA. Embo J, 2006, 25(10): 2189-2198
9. Gilljam KM, Feyzi E, Aas PA, Sousa MM, Muller R, Vagbo CB, Catterall TC, Liabakk NB, Slupphaug G, Drablos F, Krokan HE, Otterlei M. Identification of a novel, widespread, and functionally important PCNA-binding motif. J Cell Biol, 2009, 186(5): 645-654
10. Fujii T, Shimada K, Anai S, Fujimoto K, Konishi N. ALKBH2, a novel AlkB homologue, contributes to human bladder cancer progression by regulating MUC1 expression. Cancer Sci, 2013, 104(3): 321-327
11. Cetica V, Genitori L, Giunti L, Sanzo M, Bernini G, Massimino M, Sardi I. Pediatric brain tumors: mutations of two dioxygenases (hABH2 and hABH3) that directly repair alkylation damage. J Neurooncol, 2009, 94(2): 195-201
12. Johannessen TC, Prestegarden L, Grudic A, Hegi ME, Tysnes BB, Bjerkvig R. The DNA repair protein ALKBH2 mediates temozolomide resistance in human glioblastoma cells. Neuro Oncol, 2013, 15(3): 269-278
13. Mishina Y, Chen LX, He C. Preparation and characterization of the native iron(II)-containing DNA repair AlkB protein directly from Escherichia coli. J Am Chem Soc, 2004, 126(51): 16930-16936 (Pubitemid 40069508)
14. Huang H, Chopra R, Verdine GL, Harrison SC. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: Implications for drug resistance. Science, 1998, 282(5394): 1669-1675 (Pubitemid 28549275)
15. Verdine GL, Norman DP. Covalent trapping of protein-DNA complexes. Annu Rev Biochem, 2003, 72(337-366)
16. Banerjee A, Santos WL, Verdine GL. Structure of a DNA glycosylase searching for lesions. Science, 2006, 311(5764): 1153-1157
17. Yang CG, Yi C, Duguid EM, Sullivan CT, Jian X, Rice PA, He C. Crystal structures of DNA/RNA repair enzymes AlkB and ABH2 bound to dsDNA. Nature, 2008, 452(7190): 961-965 (Pubitemid 351589622)
18. Yi C, Chen B, Qi B, Zhang W, Jia G, Zhang L, Li CJ, Dinner AR, Yang CG, He C. Duplex interrogation by a direct DNA repair protein in search of base damage. Nat Struct Mol Biol, 2012, 19(7): 671-676
19. Chen B, Liu H, Sun X, Yang CG. Mechanistic insight into the recognition of single-stranded and double-stranded DNA substrates by ABH2 and ABH3. Mol Biosyst, 2010, 6(11): 2143-2149
20. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Method Enzymol, 1997, 276: 307-326 (Pubitemid 27085611)
21. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr, 1994, 50(Pt 5): 760-763
22. Read RJ. Pushing the boundaries of molecular replacement with maximum likelihood. Acta Crystallogr D Biol Crystallogr, 2001, 57(Pt 10): 1373-1382 (Pubitemid 36117185)
23. Emsley P, Cowtan K. Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr, 2004, 60(Pt 12 Pt 1): 2126-2132 (Pubitemid 41742764)
24. Yi C, Yang CG, He C. A non-heme iron-mediated chemical demethylation in DNA and RNA. Acc Chem Res, 2009, 42(4): 519-529
25. Monsen VT, Sundheim O, Aas PA, Westbye MP, Sousa MM, Slupphaug G, Krokan HE. Divergent ss-hairpins determine double-strand versus single-strand substrate recognition of human AlkB-homologues 2 and 3. Nucleic Acids Res, 2010, 38(19): 6447-6455
26. Blainey PC, van Oijen AM, Banerjee A, Verdine GL, Xie XS. A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA. Proc Natl Acad Sci U S A, 2006, 103(15): 5752-5757
27. Lin Y, Zhao T, Jian X, Farooqui Z, Qu X, He C, Dinner AR, Scherer NF. Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA. Biophys J, 2009, 96(5): 1911-1917
28. Friedman JI, Stivers JT. Detection of damaged DNA bases by DNA glycosylase enzymes. Biochemistry, 2010, 49(24): 4957-4967
29. Blainey PC, Luo GB, Kou SC, Mangel WF, Verdine GL, Bagchi B, Xie XS. Nonspecifically bound proteins spin while diffusing along DNA. Nat Struct Mol Biol, 2009, 16(12): U1224-U1234