Structural basis for recruitment of human flap endonuclease 1 to PCNA

EMBO Journal

Volumn 24, Issue 4, 2005, Pages 683-693

  Sakurai, Shigeru ^a   Kitano, Ken ^a   Yamaguchi, Hiroto ^b   Hamada, Keisuke ^a   Okada, Kengo ^a   Fukuda, Kotaro ^c   Uchida, Makiyo ^c   Ohtsuka, Eiko ^c   Morioka, Hiroshi ^c   Hakoshima, Toshio ^a,b  

^a NARA INSTITUTE OF SCIENCE AND TECHNOLOGY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c HOKKAIDO UNIVERSITY   (Japan)

Author keywords

DNA clamp; Flap endonuclease; Repair; Replication; X ray

Indexed keywords

CYCLIN DEPENDENT KINASE INHIBITOR 1; CYCLINE; FLAP ENDONUCLEASE; FLAP ENDONUCLEASE 1; UNCLASSIFIED DRUG;

ARTICLE; BETA CHAIN; CARBOXY TERMINAL SEQUENCE; COMPLEX FORMATION; CRYSTAL STRUCTURE; DNA REPAIR; DNA REPLICATION; ENZYME ACTIVITY; GENETIC STABILITY; HUMAN; HYDROPHOBICITY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; FLAP ENDONUCLEASES; HUMANS; METHANOCOCCUS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROLIFERATING CELL NUCLEAR ANTIGEN; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PYROCOCCUS FURIOSUS; SEQUENCE ALIGNMENT;

EID: 20144367589     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1038/sj.emboj.7600519     Document Type: Article

References (46)

1. Brosh Jr RM, von Kobbe C, Sommers JA, Karmakar P, Opresko PL, Piotrowski J, Dianova I, Dianov GL, Bohr VA (2001) Werner syndrome protein interacts with human flap endonuclease 1 and stimulates its cleavage activity. EMBO J 20: 5791-5801
2. 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 (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D 54: 905-921
3. Bunting KA, Roe SM, Pearl LH (2003) Structural basis for recruitment of translesion DNA polymerase Pol IV/DinB to the beta-clamp. EMBO J 22: 5883-5892
4. Ceska TA, Sayers JR, Stier G, Suck D (1996) A helical arch allowing single-stranded DNA to thread through T5 5′-exonuclease. Nature 382: 90-93
5. Chapados BR, Hosfield DJ, Han S, Qiu J, Yelent B, Shen B, Tainer JA (2004) Structural basis for FEN-1 substrate specificity and PCNA-mediated activation in DNA replication and repair. Cell 116: 39-50
6. Cip1/Waf1 disrupts the recruitment of human Fen1 by proliferating-cell nuclear antigen into the DNA replication complex. Proc Natl Acad Sci USA 93: 11597-11602
7. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D 50: 760-763
8. Dionne I, Nookala RK, Jackson SP, Doherty AJ, Bell SD (2003) A heterotrimeric PCNA in the hyperthermophilic archaeon Sulfolobus solfataricus. Mol Cell 11: 275-282
9. Friedrich-Heineken E, Hubscher U (2004) The Fen1 extrahelical 3′-flap pocket is conserved from archaea to human and regulates DNA substrate specificity. Nucleic Acids Res 32: 2520-2528
10. Fukuda K, Morioka H, Imajou S, Ikeda S, Ohtsuka E, Tsurimoto T (1995) Structure-function relationship of the eukaryotic DNA replication factor, proliferating cell nuclear antigen. J Biol Chem 270: 22527-22534
11. Gary R, Park MS, Nolan JP, Cornelius HL, Kozyreva OG, Tran HT, Lobachev KS, Resnick MA, Gordenin DA (1999) A novel role in DNA metabolism for the binding of Fen1/Rad27 to PCNA and implications for genetic risk. Mol Cell Biol 19: 5373-5382
12. Gomes XV, Burgers PM (2000) Two modes of FEN1 binding to PCNA regulated by DNA. EMBO J 19: 3811-3821
13. Gulbis JM, Kelman Z, Hurwitz J, O'Donnell M, Kuriyan J (1996) Structure of the C-terminal region of p21WAF1/CIP1 complexed with human PCNA. Cell 87: 297-306
14. Harrington JJ, Lieber MR (1994) The characterization of a mammalian DNA structure-specific endonuclease. EMBO J 13: 1235-1246
15. Henneke G, Friedrich-Heineken E, Hubscher U (2003) Flap endonuclease 1: a novel tumour suppresser protein. Trends Biochem Sci 28: 384-390
16. Hickson ID (2003) RecQ helicases: caretakers of the genome. Nat Rev Cancer 3: 169-178
17. Hingorani MM, O'Donnell M (2000) Sliding clamps: a (tail)ored fit. Curr Biol 10: R25-R29
18. Hosfield DJ, Mol CD, Shen B, Tainer JA (1998) Structure of the DNA repair and replication endonuclease and exonuclease FEN-1: coupling DNA and PCNA binding to FEN-1 activity. Cell 95: 135-140
19. Hwang KY, Baek K, Kim HY, Cho Y (1998) The crystal structure of flap endonuclease-1 from Methanococcus jannaschii. Nat Struct Biol 5: 707-713
20. Jones TA, Zou JY, Cowan SW, Kjeldgaard M (1991) Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47: 110-119
21. Kelman Z (1997) PCNA: structure, functions and interactions. Oncogene 14: 629-640
22. Kleywegt GJ, Jones TA (1997) Detecting folding motifs and similarities in protein structures. Methods Enzymol 277: 525-545
23. Klungland A, Lindahl T (1997) Second pathway for completion of human DNA base excision-repair: reconstitution with purified proteins and requirement for DNase IV (FEN1). EMBO J 16: 3341-3348
24. Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24: 946-950
25. Krishna TS, Kong XP, Gary S, Burgers PM, Kuriyan J (1994) Crystal structure of the eukaryotic DNA polymerase processivity factor PCNA. Cell 79: 1233-1243
26. Kucherlapati M, Yang K, Kuraguchi M, Zhao J, Lia M, Heyer J, Kane MF, Fan K, Russell R, Brown AM, Kneitz B, Edelmann W, Kolodner RD, Lipkin M, Kucherlapati R. (2002) Haploinsufficiency of Flap endonuclease (Fen1) leads to rapid tumor progression. Proc Natl Acad Sci USA 99: 9924-9929
27. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structure. J Appl Crystallogr 26: 283-291
28. Lawrence MC, Bourke P (2000) CONSCRIPT: a program for generating electron density isosurfaces for presentation in protein crystallography. J Appl Crystallogr 33: 990-991
29. Li X, Li J, Harrington J, Lieber MR, Burgers PM (1995) Lagging strand DNA synthesis at the eukaryotic replication fork involves binding and stimulation of FEN-1 by proliferating cell nuclear antigen. J Biol Chem 270: 22109-22112
30. Liu Y, Kao HI, Bambara RA (2004) FLAP ENDONUCLEASE 1: a central component of DNA metabolism. Annu Rev Biochem 73: 589-615
31. Maga G, Hubscher U (2003) Proliferating cell nuclear antigen (PCNA): a dancer with many partners. J Cell Sci 116: 3051-3060
32. Matsumoto Y (2001) Molecular mechanism of PCNA-dependent base excision repair. Prog Nucleic Acid Res Mol Biol 68: 129-138
33. Murante RS, Rust L, Bambara RA (1995) Calf 5′ to 3′ exo/endonuclease must slide from a 5′ end of the substrate to perform structure-specific cleavage. J Biol Chem 270: 30377-30383
34. Nicholls A, Sharp KA, Honig B (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11: 281-296
35. Oku T, Ikeda S, Sasaki H, Fukuda K, Morioka H, Ohtsuka E, Yoshikawa H, Tsurimoto T (1998) Functional sites of human PCNA which interact with p21 (Cip1/Waf1), DNA polymerase δ and replication factor C. Genes Cells 3: 357-369
36. Sakurai S, Kitano K, Okada K, Hamada K, Morioka H, Hakoshima T (2003) Preparation and crystallization of human flap endonuclease FEN-1 in complex with proliferating-cell nuclear antigen, PCNA. Acta Crystallogr D 59: 933-935
37. Shamoo Y, Steitz TA (1999) Building a replisome from interacting pieces: sliding clamp complexed to a peptide from DNA polymerase and a polymerase editing complex. Cell 99: 155-166
38. Shen B, Nolan JP, Sklar LA, Park MS (1997) Functional analysis of point mutations in human flap endonuclease-1 active site. Nucleic Acids Res 25: 3332-3338
39. Storici F, Henneke G, Ferrari E, Gordenin DA, Hubscher U, Resnick MA (2002) The flexible loop of human FEN1 endonuclease is required for flap cleavage during DNA replication and repair. EMBO J 21: 5930-5942
40. Stucki M, Jonsson ZO, Hübscher U (2001) In eukaryotic flap endonuclease 1, the C terminus is essential for substrate binding. J Biol Chem 276: 7843-7849
41. Tom S, Henricksen LA, Bambara RA (2000) Mechanism whereby proliferating cell nuclear antigen stimulates flap endonuclease 1. J Biol Chem 275: 10498-10505
42. Tsurimoto T (1998) PCNA, a multifunctional ring on DNA. Biochim Biophys Acta 1443: 23-39
43. Tsurimoto T (1999) PCNA binding proteins. Front Biosci 4: D849-D858
44. Waga S, Stillman B (1998) The DNA replication fork in eukaryotic cells. Annu Rev Biochem 67: 721-751
45. Warbrick E (1998) PCNA binding through a conserved motif. BioEssays 20: 195-199
46. Wu X, Li J, Li X, Hsieh CL, Burgers PM, Lieber MR (1996) Processing of branched DNA intermediates by a complex of human FEN-1 and PCNA. Nucleic Acids Res 24: 2036-2043