Molecular machines in archaeal DNA replication

Current Opinion in Chemical Biology

Volumn 15, Issue 5, 2011, Pages 614-619

  Beattie, Thomas R ^a   Bell, Stephen D ^a  

^a UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ARCHAEAL DNA; CYCLINE; DNA POLYMERASE; DOUBLE STRANDED DNA; HELICASE; MINICHROMOSOME MAINTENANCE PROTEIN; MINICHROMOSOME MAINTENANCE PROTEIN 7; RIBONUCLEASE; RIBONUCLEASE HII; THREONINE; UNCLASSIFIED DRUG;

ARCHAEBACTERIUM; DNA REPLICATION; ELECTRON MICROSCOPY; EUKARYOTE; MOLECULAR DYNAMICS; NONHUMAN; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN STRUCTURE; REVIEW; SULFOLOBUS SOLFATARICUS;

ARCHAEA; ARCHAEAL PROTEINS; BIOMECHANICS; DNA; DNA HELICASES; DNA REPLICATION; DNA, ARCHAEAL; DNA-BINDING PROTEINS; MODELS, MOLECULAR; PROLIFERATING CELL NUCLEAR ANTIGEN; PROTEIN INTERACTION DOMAINS AND MOTIFS; RIBONUCLEASE H;

ARCHAEA; EUKARYOTA;

EID: 80053562860     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2011.07.017     Document Type: Review

References (37)

1. Bochman M.L., Schwacha A. The Mcm complex: unwinding the mechanism of a replicative helicase. Microbiol Mol Biol Rev 2009, 73:652-683.
2. Costa A., Onesti S. Structural biology of MCM helicases. Crit Rev Biochem Mol Biol 2009, 44:326-342.
3. McGeoch A.T., Trakselis M.A., Laskey R.A., Bell S.D. Organization of the archaeal MCM complex on DNA and implications for the helicase mechanism. Nat Struct Mol Biol 2005, 12:756-762.
4. Rothenberg E., Trakselis M.A., Bell S.D., Ha T. MCM forked substrate specificity involves dynamic interaction with the 5'-tail. J Biol Chem 2007, 282:34229-34234.
5. Fletcher R.J., Bishop B.E., Leon R.P., Sclafani R.A., Ogata C.M., Chen X.J.S. The structure and function of MCM from archaeal M-thermoautotrophicum. Nat Struct Biol 2003, 10:160-167.
6. Liu W., Pucci B., Rossi M., Pisani F.M., Ladenstein R. Structural analysis of the Sulfolobus solfataricus MCM protein N-terminal domain. Nucleic Acids Res 2008, 36:3235-3243.
7. Barry E.R., McGeoch A.T., Kelman Z., Bell S.D. Archaeal MCM has separable processivity, substrate choice and helicase domains. Nucleic Acids Res 2007, 35:988-998.
8. Marinsek N., Barry E.R., Makarova K.S., Dionne I., Koonin E.V., Bell S.D. GINS, a central nexus in the archaeal DNA replication fork. EMBO Rep 2006, 7:539-545.
9. Jenkinson E.R., Chong J.P.J. Minichromosome maintenance helicase activity is controlled by N- and C-terminal motifs and requires the ATPase domain helix-2 insert. Proc Natl Acad Sci USA 2006, 103:7613-7618.
10. Brewster A.S., Wang G.G., Yu X., Greenleaf W.B., Carazo J.M., Tjajadi M., Klein M.G., Chen X.J.S. Crystal structure of a near-full-length archaeal MCM:Functional insights for an AAA+ hexameric helicase (vol 105, pg 20191, 2008). Proc Natl Acad Sci USA 2009, 106. 6023-6023.
11. Enemark E.J., Joshua-Tor L. Mechanism of DNA translocation in a replicative hexameric helicase. Nature 2006, 442:270-275.
12. Gai D.H., Zhao R., Li D.W., Finkielstein C.V., Chen X.S. Mechanisms of conformational change for a replicative hexameric helicase of SV40 large tumor antigen. Cell 2004, 119:47-60.
13. Moreau M.J., McGeoch A.T., Lowe A.R., Itzhaki L.S., Bell S.D. ATPase site architecture and helicase mechanism of an archaeal MCM. Mol Cell 2007, 28:304-314.
14. Barry E.R., Lovett J.E., Costa A., Lea S.M., Bell S.D. Intersubunit allosteric communication mediated by a conserved loop in the MCM helicase. Proc Natl Acad Sci USA 2009, 106:1051-1056.
15. Sakakibara N., Kasiviswanathan R., Melamud E., Han M., Schwarz F.P., Kelman Z. Coupling of DNA binding and helicase activity is mediated by a conserved loop in the MCM protein. Nucleic Acids Res 2008, 36:1309-1320.
16. Liew L.P., Bell S.D. The interplay of DNA binding, ATP hydrolysis and helicase activities of the archaeal MCM helicase. Biochem J 2011, 436:409-414.
17. Zhang X.D., Wigley D.B. The 'glutamate switch' provides a link between ATPase activity and ligand binding in AAA plus proteins. Nat Struct Mol Biol 2008, 15:1223-1227.
18. Mogni M.E., Costa A., Ioannou C., Bell S.D. The glutamate switch is present in all seven clades of AAA plus protein. Biochemistry 2009, 48:8774-8775.
19. Vivona J.B., Kelman Z. The diverse spectrum of sliding clamp interacting proteins. FEBS Lett 2003, 546:167-172.
20. Zhang C., Guo L., Deng L., Wu Y., Liang Y., Huang L., She Q. Revealing the essentiality of multiple archaeal pcna genes using a mutant propagation assay based on an improved knockout method. Microbiology 2010, 156:3386-3397.
21. Gulbis J.M., Kelman Z., Hurwitz J., O'Donnell M., Kuriyan J. Structure of the C-terminal region of p21(WAF1/CIP1) complexed with human PCNA. Cell 1996, 87:297-306.
22. Bubeck D., Reijns M.A., Graham S.C., Astell K.R., Jones E.Y., Jackson A.P. PCNA directs type 2 RNase H activity on DNA replication and repair substrates. Nucleic Acids Res 2011, 39:3652-3666.
23. Sakurai S., Kitano K., Yamaguchi H., Hamada K., Okada K., Fukuda K., Uchida M., Ohtsuka E., Morioka H., Hakoshima T. Structural basis for recruitment of human flap endonuclease 1 to PCNA. EMBO J 2005, 24:683-693.
24. Xing G., Kirouac K., Shin Y.J., Bell S.D., Ling H. Structural insight into recruitment of translesion DNA polymerase Dpo4 to sliding clamp PCNA. Mol Microbiol 2009, 71:678-691.
25. Mayanagi K., Kiyonari S., Nishida H., Saito M., Kohda D., Ishino Y., Shirai T., Morikawa K. Architecture of the DNA polymerase B-proliferating cell nuclear antigen (PCNA)-DNA ternary complex. Proc Natl Acad Sci USA 2011, 108:1845-1849.
26. Nishida H., Mayanagi K., Kiyonari S., Sato Y., Oyama T., Ishino Y., Morikawa K. Structural determinant for switching between the polymerase and exonuclease modes in the PCNA-replicative DNA polymerase complex. Proc Natl Acad Sci USA 2009, 106:20693-20698.
27. Pascal J.M., Tsodikov O.V., Hura G.L., Song W., Cotner E.A., Classen S., Tomkinson A.E., Tainer J.A., Ellenberger T. A flexible interface between DNA ligase and PCNA supports conformational switching and efficient ligation of DNA. Mol Cell 2006, 24:279-291.
28. Mayanagi K., Kiyonari S., Saito M., Shirai T., Ishino Y., Morikawa K. Mechanism of replication machinery assembly as revealed by the DNA ligase-PCNA-DNA complex architecture. Proc Natl Acad Sci USA 2009, 106:4647-4652.
29. Pascal J.M., O'Brien P.J., Tomkinson A.E., Ellenberger T. Human DNA ligase I completely encircles and partially unwinds nicked DNA. Nature 2004, 432:473-478.
30. Miyata T., Suzuki H., Oyama T., Mayanagi K., Ishino Y., Morikawa K. Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis. Proc Natl Acad Sci USA 2005, 102:13795-13800.
31. Georgescu R.E., Kim S.S., Yurieva O., Kuriyan J., Kong X.P., O'Donnell M. Structure of a sliding clamp on DNA. Cell 2008, 132:43-54.
32. McNally R., Bowman G.D., Goedken E.R., O'Donnell M., Kuriyan J. Analysis of the role of PCNA-DNA contacts during clamp loading. BMC Struct Biol 2010, 10:3.
33. Kiyonari S., Tahara S., Shirai T., Iwai S., Ishino S., Ishino Y. Biochemical properties and base excision repair complex formation of apurinic/apyrimidinic endonuclease from Pyrococcus furiosus. Nucleic Acids Res 2009, 37:6439-6453.
34. Dionne I., Nookala R.K., Jackson S.P., Doherty A.J., Bell S.D. A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Cell 2003, 11:275-282.
35. Beattie T.R., Bell S.D. The role of the DNA sliding clamp in Okazaki fragment maturation in archaea and eukaryotes. Biochem Soc Trans 2011, 39:70-76.
36. Moldovan G.L., Pfander B., Jentsch S. PCNA, the maestro of the replication fork. Cell 2007, 129:665-679.
37. Graham B.W., Schauer G.D., Leuba S.H., Trakselis M.A. Steric exclusion and wrapping of the excluded DNA strand occurs along discrete external binding paths during MCM helicase unwinding. Nucleic Acids Res 2011, 10.1093/nar/gkr345.