Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases

FEBS Letters

Volumn 584, Issue 15, 2010, Pages 3370-3375

  Yamasaki, Kazuhiko ^a,c   Urushibata, Yuji ^a   Yamasaki, Tomoko ^a   Arisaka, Fumio ^b   Matsui, Ikuo ^a  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^c NB Health Laboratory   (Japan)

Author keywords

AAA+ ATPase; Archaea; DNA polymerase; Evolution; Exonuclease; NMR

Indexed keywords

D FAMILY DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE ALPHA; DNA DIRECTED DNA POLYMERASE EPSILON; DNA POLYMERASE; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ARCHAEBACTERIUM; ARTICLE; BETA SHEET; ENZYME STRUCTURE; EUKARYOTE; MOLECULAR EVOLUTION; NUCLEAR MAGNETIC RESONANCE; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN FOLDING;

ADENOSINE TRIPHOSPHATASES; AMINO ACID SEQUENCE; DNA-DIRECTED DNA POLYMERASE; EUKARYOTA; EVOLUTION, MOLECULAR; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; MOLECULAR SEQUENCE DATA; PROTEIN MULTIMERIZATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEIN SUBUNITS; PYROCOCCUS HORIKOSHII; SOLUTIONS; ULTRACENTRIFUGATION;

ARCHAEA; EUKARYOTA;

EID: 77955268031     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2010.06.026     Document Type: Article

References (33)

1. Cann I.K., Komori K., Toh H., Kanai S., Ishino Y. A heterodimeric DNA polymerase: evidence that members of Euryarchaeota possess a distinct DNA polymerase. Proc. Natl Acad. Sci. USA 1998, 95:14250-14255.
2. Ishino Y., Komori K., Cann I.K., Koga Y. A novel DNA polymerase family found in Archaea. J. Bacteriol. 1998, 180:2232-2236.
3. Shen Y., Musti K., Hiramoto M., Kikuchi H., Kawarabayasi Y., Matsui I. Invariant Asp-1122 and Asp-1124 are essential residues for polymerization catalysis of family D DNA polymerase from Pyrococcus horikoshii. J. Biol. Chem. 2001, 276:27376-27383.
4. Aravind L., Koonin E.V. Phosphoesterase domains associated with DNA polymerases of diverse origins. Nucleic Acids Res. 1998, 26:3746-3752.
5. Mäkiniemi M., Pospiech H., Kilpeläinen S., Jokela M., Vihinen M., Syväoja J.E. A novel family of DNA-polymerase-associated B subunits. Trends Biochem. Sci. 1999, 24:14-16.
6. Nuutinen T., Tossavainen H., Fredriksson K., Pirilä P., Permi P., Pospiech H., Syvaoja J.E. The solution structure of the amino-terminal domain of human DNA polymerase ε subunit B is homologous to C-domains of AAA+ proteins. Nucleic Acids Res. 2008, 36:5102-5110.
7. +: a class of chaperonine-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 1999, 9:27-43.
8. Baranovskiy A., Babayeva N.D., Liston V.G., Rogozin I.B., Koonin E.V., Pavlov Y.I., Vassylyev D.G., Tahirov T.H. X-ray structure of the complex of regulatory subunits of human DNA polymerase δ. Cell Cycle 2008, 7:3026-3036.
9. Shen Y., Tang X.-F., Matsui I. Subunit interaction and regulation of activity through terminal domains of the family D DNA polymerase from Pyrocossus horikoshii. J. Biol. Chem. 2003, 278:21247-21257.
10. Tang X.-F., Shen Y., Matsui E., Matsui I. Domain topology of the DNA polymerase D complex from a hyperthermophilic archaeon Pyrocossus horikoshii. Biochemistry 2004, 43:11818-11827.
11. Neiderhardt F.C., Bloch P.L., Smith D.F. Culture medium for exchange processes to two-dimensional NMR spectroscopy. J. Chem. Phys. 1974, 71:4546-4553.
12. Pace C.N., Vajdos F., Fee L., Grimsley G., Gray T. How to measure and predict the molar absorption coefficient of a protein. Prot. Sci. 1995, 4:2411-2423.
13. Wüthrich K. NMR of Proteins and Nucleic Acids 1986, John Wiley & Sons Inc., New York.
14. Bax A. Multidimensional nuclear magnetic resonance methods for protein studies. Curr. Opin. Struct. Biol. 1994, 4:738-744.
15. Yamasaki K., Kigawa T., Inoue M., Tateno M., Yamasaki T., Yabuki T., Aoki M., Seki E., Matsuda T., Nunokawa E., Ishizuka Y., Terada T., Shirouzu M., Osanai T., Tanaka A., Seki M., Shinozaki K., Yokoyama S. A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors. J. Mol. Biol. 2004, 337:49-63.
16. Kay L.E., Bax A. New methods for measurement of NH-CαH coupling constants in 15N-labelled proteins. J. Magn. Reson. 1989, 86:110-126.
17. Nilges M., Clore G.M., Gronenborn A.M. Determination of the three-dimensional structures of proteins from inter-proton distance data by dynamic simulated annealing from a random array of atoms. FEBS Lett. 1988, 239:129-136.
18. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuzewski J., Nilges M., Pannu N.S., Read R.J., Rice L.M., Simonson T., Warren G.L. Crystallography and NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr., Sect. D 1998, 54:905-921.
19. Laue T.M., Shah B.D., Ridgeway T.M., Pelletier S.L. Computer-aided Interpretation of Analytical Sedimentation Data for Proteins. Analytical Ultracentrifugation in Biochemistry and Polymer Science 1992, 90-125. Royal Society of Chemistry, Cambridge, United Kingdom. S.E. Harding, A.J. Rowe, J.C. Horton (Eds.).
20. Woody R.W. Circular dichroism. Methods Enzymol. 1995, 246:34-71.
21. Morikawa M., Izawa Y., Rashid N., Hoaki T., Imanaka T. Purification and characterization of a thermostable thiol protease from a newly isolated hyperthermophilic Pyrococcus sp. Appl. Environ. Microbiol. 1994, 60:4559-4566.
22. González J.M., Masuchi Y., Robb F.T., Ammerman J.W., Maeder D.L., Yanagibayashi M., Tamaoka J., Kato C. Pyrococcus horikoshii sp Nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa. Trouch. Extremophiles 1998, 2:123-130.
23. Fiala G., Stetter K.O. Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100 C. Arch. Microbiol. 1986, 145:56-61.
24. Darland G., Brock T.D., Samsonoff W., Conti S.F. A thermophilic, acidophilic mycoplasma isolated from a coal refuse pile. Science 1970, 170:1416-1418.
25. Zeikus J.G., Wolfe R.S. Methanobacterium thermoautotrophicus sp. n., an anaerobic, autotrophic, extreme thermophile. J. Bacteriol. 1972, 109:707-713.
26. Jones W.J., Leigh J.A., Mayer F., Woese C.R., Wolfe R.S. Methanococcus jannaschii sp. nov., an extremely thermophilic methanogen from a submarine hydrothermal vent. Arch. Microbiol. 1983, 136:254-261.
27. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 1993, 233:123-138.
28. Jeruzalmi D., Yurieva O., Zhao Y., Young M., Stewart J., Hingorani M., O'Donnel M., Kuriyan J. Mechanism of processivity clamp opening by the delta subunit wrench of the clamp loader complex of E. coli DNA polymerase III. Cell 2001, 106:417-428.
29. Putnam C.D., Clancy S.B., Tsuruta H., Gonzalez S., Wetmur J.G., Tainer J.A. Structure and mechanism of the RuvB holliday junction branch migration motor. J. Mol. Biol. 2001, 311:297-310.
30. Koradi R., Billeter M., Wüthrich K. MOLMOL: a program for display and analysis of macromolecular structures. J. Mol. Graph. 1996, 14:51-55.
31. Tahirov T.H., Makorava K.S., Rogozin I.B., Pavlov Y.I., Koonin E.V. Evolution of DNA polymerases: and inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polymerases from two classes of archaeal ancestors. Biol. Direct 2009, 4:1-11.
32. Laskowski R.A., Rullmann J.A.C., MacArthur W.M., Kaptein R., Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 1996, 8:477-486.
33. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., Higgins D.G. The CLUSTAL-X windows interface. flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 1997, 25:4876-4882.