Biochemical characterization of an ATP-dependent DNA ligase from the hyperthermophilic crenarchaeon Sulfolobus shibatae

Extremophiles

Volumn 6, Issue 6, 2002, Pages 469-477

  Lai, Xiaoqin ^a   Shao, Hongbing ^b   Hao, Fuying ^b   Huang, Li ^a  

^a INSTITUTE OF MICROBIOLOGY   (China)

^b PEKING UNIVERSITY   (China)

Author keywords

ATP; Crenarchaeota; DNA ligase; Metal cofactor; Sulfolobus shibatae; Thermostability

Indexed keywords

ARCHAEA; CRENARCHAEOTA; ESCHERICHIA COLI; SULFOLOBUS; SULFOLOBUS SHIBATAE;

ADENOSINE TRIPHOSPHATE; BACTERIAL DNA; BACTERIAL PROTEIN; DIVALENT CATION; HYBRID PROTEIN; NUCLEOTIDE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; POLYDEOXYRIBONUCLEOTIDE SYNTHASE (ATP); PRIMER DNA; SINGLE STRANDED DNA; VIRUS DNA;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL GENE; BACTERIOPHAGE M13; COMPARATIVE STUDY; ENZYME SPECIFICITY; ENZYMOLOGY; ESCHERICHIA COLI; GENETICS; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR CLONING; MOLECULAR GENETICS; PH; PROTEIN MOTIF; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; SULFOLOBUS; TEMPERATURE;

ADENOSINE TRIPHOSPHATE; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BACTERIOPHAGE M13; CATIONS, DIVALENT; CLONING, MOLECULAR; DNA LIGASES; DNA PRIMERS; DNA, BACTERIAL; DNA, SINGLE-STRANDED; DNA, VIRAL; ESCHERICHIA COLI; GENES, BACTERIAL; HYDROGEN-ION CONCENTRATION; MOLECULAR SEQUENCE DATA; NUCLEOTIDES; RECOMBINANT FUSION PROTEINS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SUBSTRATE SPECIFICITY; SULFOLOBUS; TEMPERATURE;

EID: 0142096802     PISSN: 14310651     EISSN: 14334909     Source Type: Journal    
DOI: 10.1007/s00792-002-0284-5     Document Type: Article

References (33)

1. Aravind L, Koonin EV (1999) Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J Mol Biol 287:1023-1040
2. Bradford MM (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248-254
3. Brock TD, Brock KM, Belly RT, Weiss RL (1972) Sulfolobus: a new genus of sulfur-oxidizing bacteria living at low pH and high temperature. Arch Mikrobiol 84:54-68
4. Cheng C, Shuman S (1997) Characterization of an ATP-dependent DNA ligase encoded by Haemophilus influenzae. Nucleic Acids Res 25:1369-1374
5. Clark DJ, Felsenfeld G (1991) Formation of nucleosomes on positively supercoiled DNA. EMBO J 10:387-395
6. Doherty AJ, Dafforn TR (2000) Nick recognition by DNA ligases. J Mol Biol 296:43-56
7. Doherty AJ, Suh SW (2000) Structural and mechanistic conservation in DNA ligases. Nucleic Acids Res 28:4051-4058
8. Doherty AJ, Wigley DB (1999) Functional domains of an ATP-dependent DNA ligase. J Mol Biol 285:63-71
9. Edgell DR, Doolittle WF (1997) Archaea and the origin (s) of DNA replication proteins. Cell 89:995-998
10. Engler MJ, Richardson CC (1982) DNA ligases. In: Boyer PD (ed) The enzymes, vol. 15. Academic. New York, pp 3-29
11. Grogan DW (1989) Phenotypic characterization of the archaebacterial genus Sulfolobus: comparison of five wild-type strains. J Bacteriol 171:6710-6719
12. Husain I, Tomkinson AE, Burkhart WA, Moyer MB, Ramos W, Mackey ZB, Besterman JM, Chen J (1995) Purification and characterization of DNA ligase III from bovine testes. Homology with DNA ligase II and vaccinia DNA ligase. J Biol Chem 270:9683-9690
13. Kletzin A (1992) Molecular characterisation of a DNA ligase gene of the extremely thermophilic archaeon Desulfurolobus ambivalens shows close phylogenetic relationship to eukaryotic ligases. Nucleic Acids Res 20:5389-5396
14. Lee JY, Chang C, Song HK, Moon J, Yang JK, Kim HK, Kwon ST, Suh SW (2000) Crystal structure of NAD (+)-dependent DNA ligase: modular architecture and functional implications. EMBO J 19:1119-1129
15. Lehman IR (1974) DNA ligase: structure, mechanism, and function. Science 186:790-797
16. Lindahl T, Barnes DE (1992) Mammalian DNA ligases. Annu Rev Biochem 61:251-281
17. Lineweaver H, Burk D (1934) The determination of enzyme dissociation constants. J Am Chem Soc 56:658-666
18. Mai VQ, Chen X, Hong R, Huang L (1998) Small abundant DNA binding proteins from the thermoacidophilic archaeon Sulfolobus shibatae constrain negative DNA supercoils. J Bacteriol 180:2560-2563
19. Montecucco A, Lestingi M, Pedrali-Noy G, Spadari S, Ciarrocchi G (1990) Use of ATP, dATP and their alpha-thio derivatives to study DNA ligase adenylation. Biochem J 271:265-268
20. Nakatani M, Ezaki S, Atomi H, Imanaka T (2000) A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity. J Bacteriol 182:6424-6433
21. Odell M, Sriskanda V, Shuman S, Nikolov DB (2000) Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining. Mol Cell 6:1183-1193
22. Olmsted JB (1981) Affinity purification of antibodies from diazotized paper blots of heterogeneous protein samples. J Biol Chem 256:11955-11957
23. Olsen GJ, Woese CR (1997) Archaeal genomics: an overview. Cell 89:991-994
24. She Q, Singh RK, Confalonieri F, Zivanovic Y, Allard G, Awayez MJ, Chan-Weiher CC, Clausen IG, Curtis BA, De Moors A, Erauso G, Fletcher C, Gordon PM, Heikamp-de Jong I, Jeffries AC, Kozera CJ, Medina N, Peng X, Thi-Ngoc HP, Redder P, Schenk ME, Theriault C, Tolstrup N, Charlebois RL, Doolittle WF, Duguet M, Gaasterland T, Garrett RA, Ragan MA, Sensen CW, Van der Oost J (2001) The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci USA 98:7835-7840
25. Shuman S (1995) Vaccinia virus DNA ligase: specificity, fidelity, and inhibition. Biochemistry 34:16138-16147
26. Singleton MR, Hakansson K, Timson DJ, Wigley DB (1999) Structure of the adenylation domain of an NAD+-dependent DNA ligase. Structure Fold Des 7:35-42
27. Sriskanda V, Shuman S (1998) Mutational analysis of Chlorella virus DNA ligase: catalytic roles of domain I and motif VI. Nucleic Acids Res 26:4618-4625
28. Sriskanda V, Kelman Z, Hurwitz J, Shuman S (2000) Characterization of an ATP-dependent DNA ligase from the thermophilic archaeon Methanobacterium thermoautotrophicum. Nucleic Acids Res 28:2221-2228
29. Subramanya HS, Doherty AJ, Ashford SR, Wigley DB (1996) Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7. Cell 85:607-615
30. Takahashi M, Yamaguchi E, Uchida T (1984) Thermophilic DNA ligase. Purification and properties of the enzyme from Thermus thermophilus HB8. J Biol Chem 259:10041-10047
31. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
32. Tong J, Barany F, Cao W (2000) Ligation reaction specificities of an NAD (+)-dependent DNA ligase from the hyperthermophile Aquifex aeolicus. Nucleic Acids Res 28:1447-1454
33. Wu DY, Wallace RB (1989) Specificity of the nick-closing activity of bacteriophage T4 DNA ligase. Gene 76:245-254