Crystal structure of a putative DNA methylase TTHA0409 from Thermus thermophilus HB8

Proteins: Structure, Function and Genetics

Volumn 73, Issue 1, 2008, Pages 259-264

  Morita, Rihito ^a   Ishikawa, Hirohito ^a   Nakagawa, Noriko ^a,b   Kuramitsu, Seiki ^a,b   Masui, Ryoji ^a,b  

^a OSAKA UNIVERSITY   (Japan)

^b Harima Institute ^*  (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER; DNA METHYLTRANSFERASE;

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLIZATION; ENZYME STRUCTURE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; THERMUS THERMOPHILUS;

CLONING, MOLECULAR; CRYSTALLIZATION; DIMERIZATION; DNA MODIFICATION METHYLASES; PROTEIN CONFORMATION; SUBSTRATE SPECIFICITY; THERMUS THERMOPHILUS;

THERMUS THERMOPHILUS;

EID: 50849083544     PISSN: 08873585     EISSN: 10970134     Source Type: Journal    
DOI: 10.1002/prot.22158     Document Type: Article

References (33)

1. Wilson GG, Murray NE. Restriction and modification systems. Annu Rev Genet 1991;25:585-627.
2. Bickle TA, Kruger DH. Biology of DNA restriction. Microbiol Rev 1993;57:434-450.
3. Sistla S, Rao DN. S-Adenosyl-L-methionine-dependent restriction enzymes. Crit Rev Biochem Mol Biol 2004;39:1-19.
4. Bujnicki JM. Understanding the evolution of restriction-modification systems: clues from sequence and structure comparisons. Acta Biochim Pol 2001;48:935-967.
5. Cheng X. Structure and function of DNA methyltransferases. Annu Rev Biophys Biomol Struct 1995;24:293-318.
6. Jeltsch A. Beyond Watson and Crick: DNA methylation and molecular enzymology of DNA methyltransferases. Chem Bio Chem 2002; 3:274-293.
7. Ahmad I, Rao DN. Chemistry and biology of DNA methyltransferases. Crit Rev Biochem Mol Biol 1996;31:361-380.
8. Malone T, Blumenthal RM, Cheng X. Structure-guided analysis reveals nine sequence motifs conserved among DNA aminomethyltransferases and suggests a catalytic mechanism for these enzymes. J Mol Biol 1995;253:618-632.
9. Yokoyama S, Hirota H, Kigawa T, Yabuki T, Shirouzu M, Terada T, Ito Y, Matsuo Y, Kuroda Y, Nishimura Y, Kyogoku Y, Miki K, Masui R, Kuramitsu S. Structural genomics projects in Japan. Nat Struct Biol 2000;7:943-945.
10. Yokoyama S, Matsuo Y, Hirota H, Kigawa T, Shirouzu M, Kuroda Y, Kurumizaka H, Kawaguchi S, Ito Y, Shibata T, Kainosho M, Nishimura Y, Inoue Y, Kuramitsu S. Structural genomics projects in Japan. Prog Biophys Mol Biol 2000;73:363-376.
11. Oshima T, Imahori K. Description of Thermus thermophilus (Yoshida and Oshima) comb. nov. A non-sporulating thermophilic bacterium from a Japanese thermal spa. Int J Syst Bacteriol 1974;24:102-112.
12. Sato S, Nakazawa K, Shinomiya T. A DNA methylase from Thermus thermophilus HB8. J Biochem 1980;88:737-747.
13. Sasaki C, Sugiura I, Ebihara A, Tamura T, Sugio S, Inagaki K. The crystal structure of hypothetical methyltransferase from Thermus thermophilus HB8. Proteins 2006;64:552-557.
14. Banerjee S, Chowdhury R. An orphan DNA (cytosine-5-)-methyltransferase in Vibrio cholerae. Microbiology 2006;152:1055-1062.
15. Otwinowski Z, Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 1991;276:307-325.
16. Terwilliger TC, Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 1999;55:849-861.
17. Terwilliger TC. Maximum-likelihood density modification. Acta Crystallogr D Biol Crystallogr 2000;56:965-972.
18. McRee DE. A visual protein crystallographic software system for X11/XView. J Mol Graph 1992;10:44-46.
19. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL. Crystallography and NMR System: a new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr 1998;54:905-921.
20. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 1994;50:760-763.
21. Cheng X, Roberts RJ. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res 2001;29:3784-3795.
22. Martin JL, McMillan FM. SAM (dependent) I AM: the S-adenosyl- methionine-dependent methyltransferase fold. Curr Opin Struct Biol 2002;12:783-793.
23. Bheemanaik S, Reddy YV, Rao DN. Structure, function and mechanism of exocyclic DNA methyltransferases. Biochem J 2006;399: 177-190.
24. Gong W, O'Gara M, Blumenthal RM, Cheng X. Structure of PvuII DNA-(cytosine N4) methyltransferase, an example of domain permutation and protein fold assignment. Nucleic Acids Res 1997; 25:2702-2715.
25. Scavetta RD, Thomas CB, Walsh MA, Szegedi S, Joachimiak A, Gumport RI, Churchill ME. Structure of RsrI methyltransferase, a member of the N6-adenine β class of DNA methyltransferases. Nucleic Acids Res 2000;28:3950-3961.
26. Thomas CB, Scavetta RD, Gumport RI, Churchill ME. Structures of liganded and unliganded RsrI N6-adenine DNA methyltransferase: a distinct orientation for active cofactor binding. J Biol Chem 2003;278:26094-26101.
27. Osipiuk J, Walsh MA, Joachimiak A. Crystal structure of MboIIA methyltransferase. Nucleic Acids Res 2003;31:5440-5448.
28. Lokanath NK, Shiromizu I, Ohshima N, Nodake Y, Sugahara M, Yokoyama S, Kuramitsu S, Miyano M, Kunishima N. Structure of aldolase from Thermus thermophilus HB8 showing the contribution of oligomeric state to thermostability. Acta Crystallogr D Biol Crystallogr 2004;60:1816-1823.
29. Thomas CB, Gumport RI. Dimerization of the bacterial RsrI N6- adenine DNA methyltransferase. Nucleic Acids Res 2006;34:806-815.
30. Takahashi N, Naito Y, Handa N, Kobayashi I. A DNA methyltransferase can protect the genome from postdisturbance attack by a restriction-modification gene complex. J Bacteriol 2006;184:6100-6108.
31. 6-methyladenine. Nucleic Acids Res 1985;13:1399-1412.
32. 4- Methylcytosine as a minor base in bacterial DNA. J Bacteriol 1987;169:939-943.
33. Ehrlich M, Norris KF, Wang RY, Kuo KC, Gehrke CW. DNA cytosine methylation and heat-induced deamination. Biosci Rep 1986;6: 387-393.