Sequence context effect for hMSH2-hMSH6 mismatch-dependent activation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 106, Issue 11, 2009, Pages 4177-4182

  Mazurek, Anthony ^a,c   Johnson, Christopher N ^b   Germann, Markus W ^b   Fishel, Richard ^a  

^a OHIO STATE UNIVERSITY   (United States)

^b GEORGIA STATE UNIVERSITY   (United States)

^c Simons Center for Quantitative Biology   (United States)

Author keywords

ATPase; Hereditary nonpolyposis colon cancer; Human mismatch repair; MutS homologs

Indexed keywords

ADENOSINE TRIPHOSPHATASE; DNA; INTERMEDIN; OLIGONUCLEOTIDE; PROTEIN MSH2; PROTEIN MSH6; PROTEIN MUTS; PROTON; PURINE; PYRIMIDINE; SOLVENT;

ACCURACY; ARTICLE; BASE MISPAIRING; CONTROLLED STUDY; ENZYME ACTIVATION; ENZYME ACTIVITY; MISMATCH REPAIR; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FUNCTION; SEQUENCE HOMOLOGY;

ADENOSINE TRIPHOSPHATASES; BASE PAIR MISMATCH; BASE SEQUENCE; DNA REPAIR; DNA-BINDING PROTEINS; ENZYME ACTIVATION; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MUTS HOMOLOG 2 PROTEIN; NUCLEIC ACID CONFORMATION; PURINES; PYRIMIDINES;

EID: 63149199448     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0808572106     Document Type: Article

References (49)

1. Kolodner R (1996) Biochemistry and genetics of eukaryotic mismatch repair. Genes Dev 10:1433-1442.
2. Boland CR, Fishel R (2005) Lynch syndrome: Form, function, proteins, and basketball. Gastroenterology 129:751-755.
3. Ban C, Yang W (1998) Crystal structure and ATPase activity of MutL: Implications for DNA repair and mutagenesis. Cell 95:541-552.
4. Haber LT, Walker GC (1991) Altering the conserved nucleotide binding motif in the Salmonella typhimurium MutS mismatch repair protein affects both its ATPase and mismatch binding activities. EMBO J 10:2707-2715.
5. Gradia S, Acharya S, Fishel R (1997) The human mismatch recognition complex hMSH2- hMSH6 functions as a novel molecular switch. Cell 91:995-1005.
6. Su S-S, Modrich P (1986) Escherichia coli mutS-encoded protein binds to mismatched DNA base pairs. Proc Natl Acad Sci USA 83:5057-5061.
7. GradiaS,AcharyaS,Fishel R(2000)Theroleofmismatchednucleotidesin activating the hMSH2-hMSH6 molecular switch. J Biol Chem 275:3922-3930.
8. Karran P, Marinus MG (1982) Mismatch correction at O6-methylguanine residues in E. coli DNA. Nature 296:868-869.
9. Ni TT, Marsischky GT, Kolodner RD (1999) MSH2 and MSH6 are required for removal of adenine misincorporated opposite 8-oxo-guanine in S. cerevisiae. Mol Cell 4:439-444.
10. Lindahl T(2001)Keynote: Past, present,and future aspects of base excision repair. Prog Nucleic Acid Res Mol Biol 68:xvii-xxx.
11. Natrajan G., et al. (2003) Structures of Escherichia coli DNA mismatch repair enzyme MutS in complex with different mismatches: A common recognition mode for diverse substrates. Nucleic Acids Res 31:4814-4821.
12. Lamers MH, et al. (2000) The crystal structure of DNA mismatch repair protein MutS binding to a G × T mismatch. Nature 407:711-717.
13. Obmolova G, Ban C, Hsieh P, Yang W (2000) Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA. Nature 407:703-710.
14. Warren JJ, et al. (2007) Structure of the human MutSalpha DNA lesion recognition complex. Mol Cell 26:579-592.
15. Schofield MJ, et al. (2001) The Phe-X-Glu DNA binding motif of MutS. The role of hydrogen bonding in mismatch recognition. J Biol Chem 276:45505-45508.
16. Isaacs RJ, Rayens WS, Spielmann HP (2002) Structural differences in the NOE-derived structure of G-T mismatched DNA relative to normal DNA are correlated with differences in (13)C relaxation-based internal dynamics. J Mol Biol 319:191-207.
17. Kool ET(2001)Hydrogen bonding, base stacking, and steric effects in DNA replication. Annu Rev Biophys Biomol Struct 30:1-22.
18. Allawi HT,Santa Lucia J, Jr (1997) Thermodynamics and NMR of internal G.T mismatches in DNA. Biochemistry 36:10581-10594.
19. Hunter CA (1993) Sequence-dependent DNA structure. The role of base stacking interactions. J Mol Biol 230:1025-1054.
20. Yakovchuk P, Protozanova E, Frank-Kamenetskii MD (2006) Base-stacking and base- pairing contributions in to thermal stability of the DNA double helix. Nucleic Acids Res 34:564-574.
21. Jones M, Wagner R, Radman M (1987) Repair of a mismatch is influenced by the base composition of the surrounding nucleotide sequence. Genetics 115:605-610.
22. Marsischky GT, Kolodner RD (1999) Biochemical characterization of the interaction between the Saccharomyces cerevisiae MSH2-MSH6 complex and mispaired bases in DNA. J Biol Chem 274:26668-26682.
23. Wang H, Lawrence CW, Li GM, Hays JB (1999) Specific binding of human MSH2.MSH6 mismatch-repair protein heterodimers to DNA incorporating thymine- or uracil- containing UV light photoproducts opposite mismatched bases. J Biol Chem 274:16894-16900.
24. Kolodner RD, Mendillo ML, Putnam CD (2007) Coupling distant sites in DNA during DNA mismatch repair. Proc Natl Acad Sci USA 104:12953-12954.
25. Holmes J, Jr, Clark S, Modrich P (1990) Strand-specific mismatch correction in nuclear extracts of human and Drosophila melanogaster cell lines. Proc Natl Acad Sci USA 87:5837-5841.
26. Thomas DC, Roberts JD, Kunkel TA (1991) Heteroduplex repair in extracts of human HeLa cells. J Biol Chem 266:3744-3751.
27. Constantin N, Dzantiev L, Kadyrov FA, Modrich P (2005) Human mismatch repair: Reconstitution of a nick-directed bidirectional reaction. J Biol Chem 280:39752-39761.
28. Zhang Y, et al. (2005) Reconstitution of 5′-directed human mismatch repair in a purified system. Cell 122:693-705.
29. Gradia S, et al. (1999) hMSH2-hMSH6 forms a hydrolysis-independent sliding clamp on mismatched DNA. Mol Cell 3:255-261.
30. Acharya S, Foster PL, Brooks P, Fishel R (2003) The coordinated functions of the E. coli MutS and MutL proteins in mimsatch repair. Mol Cell 12:233-246.
31. Mendillo ML, Mazur DJ, Kolodner RD (2005) Analysis of the interaction between the Saccharomyces cerevisiae MSH2-MSH6 and MLH1-PMS1 complexes with DNA using a reversible DNA end-blocking system. J Biol Chem 280:22245-22257.
32. Fang WH, Modrich P (1993) Human strand-specific mismatch repair occurs by a bidirectional mechanism similar to that of the bacterial reaction. J Biol Chem 268:11838-11844.
33. Allawi HT, SantaLucia J, Jr (1998) Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: Sequence dependence and pH effects. Biochemistry 37:9435-9444.
34. Allawi HT, SantaLucia J, Jr (1998) Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. Biochemistry 37:2170-2179.
35. Allawi HT, SantaLucia J, Jr (1998) Thermodynamics of internal C.T mismatches in DNA. Nucleic Acids Res 26:2694-2701.
36. Wuthrich K (1986) NMR of Proteins and Nucleic Acids (Wiley, New York).
37. Gorenstein DG (1994) Conformational dynamics of DNA and protein-DNA complexes by 31P NMR. Chem Rev 94:1315-1338.
38. Aramini JM, Cleaver SH, Pon RT, Cunningham RP, Germann MW (2004) Solution structure of a DNA duplex containing an alpha-anomeric adenosine: Insights into substrate recognition by endonuclease IV. J Mol Biol 338:77-91.
39. Fazakerley, et al. (1986) Structures of mismatched base pairs in DNA and their recognition by the Escherichia coli mismatch repair system. EMBO J 5:3697-3703.
40. Patel DJ, Kozlowski SA, Ikuta S, Itakura K (1984) Dynamics of DNA duplexes containing internal G-T, G-A, A-C, and T-C pairs: Hydrogen exchange at and adjacent to mismatch sites. Fed Proc. 43:2663-2670.
41. Gueron M, Leroy JL (1995) Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol 261:383-413.
42. Moe JG, Russu IM (1992) Kinetics and energetics of base-pair opening in 5′- d(CGCGAATTCGCG)-3′ and a substituted dodecamer containing G.T mismatches. Biochemistry 31:8421-8428.
43. Yang W (2006) Poor base stacking at DNA lesions may initiate recognition by many repair proteins. DNA Repair 5:654-666.
44. SantaLucia J, Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95:1460-1465.
45. Packer MJ, Dauncey MP, Hunter CA (2000) Sequence-dependent DNA structure: Tet- ranucleotide conformational maps. J Mol Biol 295:85-103.
46. Kunkel TA, Erie DA (2005) DNA mismatch repair. Annu Rev Biochem 74:681-710.
47. Mazurek A, Berardini M, Fishel R (2002) Activation of human MutS homologs by 8-oxo-guanine DNA damage. J Biol Chem 277:8260-8266.
48. Aramini JM, Kalisch BW, Pon RT, van de Sande JH, Germann MW (1996) Structure of a DNA duplex that contains alpha-anomeric nucleotides and 3′-3′ and 5′-5′ phosphodiester linkages: Coexistence of parallel and antiparallel DNA. Biochemistry 35:9355-9365.
49. Eisenthal R, Danson MJ, Hough DW (2007) Catalytic efficiency and kcat/Km: A useful comparator? Trends Biotechnol 25:247-249.