Crystal structure of yeast DNA polymerase ε catalytic domain

PLoS ONE

Volumn 9, Issue 4, 2014, Pages

  Jain, Rinku ^a   Rajashankar, Kanagalaghatta R ^b   Buku, Angeliki ^a   Johnson, Robert E ^c   Prakash, Louise ^c   Prakash, Satya ^c   Aggarwal, Aneel K ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b Department of Molecular Biology and Genetics   (United States)

^c University of Texas Medical Branch School of Medicine   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CALCIUM ION; DNA; DNA DIRECTED DNA POLYMERASE EPSILON; EXONUCLEASE; PURINE; PYRIMIDINE; 2'-DEOXYCYTIDINE 5'-TRIPHOSPHATE; DEOXYCYTIDINE PHOSPHATE; DNA DIRECTED DNA POLYMERASE ALPHA;

AMINO TERMINAL SEQUENCE; ARTICLE; BASE PAIRING; CONTROLLED STUDY; CRYSTAL STRUCTURE; CRYSTALLIZATION; DNA SYNTHESIS; ENZYME ACTIVE SITE; ENZYME ANALYSIS; ENZYME REGULATION; ENZYME STRUCTURE; NONHUMAN; PROTEIN DOMAIN; PROTEIN FOLDING; SACCHAROMYCES CEREVISIAE; CHEMISTRY; ENZYMOLOGY; METABOLISM; STRUCTURAL HOMOLOGY; X RAY CRYSTALLOGRAPHY;

CATALYTIC DOMAIN; CRYSTALLOGRAPHY, X-RAY; DEOXYCYTOSINE NUCLEOTIDES; DNA POLYMERASE II; SACCHAROMYCES CEREVISIAE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 84899660104     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0094835     Document Type: Article

References (36)

1. Johnson A, O'Donnell M (2005) Cellular DNA replicases: components and dynamics at the replication fork. Annu Rev Biochem 74: 283-315.
2. Johansson E, Macneill SA (2010) The eukaryotic replicative DNA polymerases take shape. Trends Biochem Sci 35: 339-347.
3. Briggs S, Tomlinson I (2013) Germline and somatic polymerase epsilon and delta mutations define a new class of hypermutated colorectal and endometrial cancers. J Pathol 230: 148-153.
4. Palles C, Cazier JB, Howarth KM, Domingo E, Jones AM, et al. (2013) Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nat Genet 45: 136-144.
5. (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature 487: 330-337.
6. Kandoth C, Schultz N, Cherniack AD, Akbani R, Liu Y, et al. (2013) Integrated genomic characterization of endometrial carcinoma. Nature 497: 67-73.
7. Perera RL, Torella R, Klinge S, Kilkenny ML, Maman JD, et al. (2013) Mechanism for priming DNA synthesis by yeast DNA Polymerase alpha. Elife 2: e00482.
8. Swan MK, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2009) Structural basis of high-fidelity DNA synthesis by yeast DNA polymerase delta. Nat Struct Mol Biol 16: 979-986.
9. Hogg M, Osterman P, Bylund GO, Ganai RA, Lundstrom EB, et al. (2014) Structural basis for processive DNA synthesis by yeast DNA polymerase epsilon. Nat Struct Mol Biol 21: 49-55.
10. Jain R, Vanamee ES, Dzikovski BG, Buku A, Johnson RE, et al. (2014) An Iron-Sulfur Cluster in the Polymerase Domain of Yeast DNA Polymerase epsilon. J Mol Biol 426: 301-308.
11. Franklin MC, Wang J, Steitz TA (2001) Structure of the replicating complex of a pol alpha family DNA polymerase. Cell 105: 657-667.
12. Doublie S, Tabor S, Long AM, Richardson CC, Ellenberger T (1998) Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution [see comments]. Nature 391: 251-258.
13. Li Y, Korolev S, Waksman G (1998) Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation. Embo J 17: 7514-7525.
14. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2005) Rev1 employs a novel mechanism of DNA synthesis using a protein template. Science 309: 2219-2222.
15. Rothwell PJ, Waksman G (2005) Structure and mechanism of DNA polymerases. Adv Protein Chem 71: 401-440.
16. YangW(2011) Nucleases: diversity of structure, function and mechanism. Q Rev Biophys 44: 1-93.
17. Beese LS, Steitz TA (1991) Structural basis for the 39-59 exonuclease activity of Escherichia coli DNA polymerase I: a two metal ion mechanism. EMBO J 10: 25-33.
18. Freemont PS, Friedman JM, Beese LS, Sanderson MR, Steitz TA (1988) Cocrystal structure of an editing complex of Klenow fragment with DNA. Proc Natl Acad Sci U S A 85: 8924-8928.
19. 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.
20. Lone S, Townson SA, Uljon SN, Johnson RE, Brahma A, et al. (2007) Human DNA polymerase kappa encircles DNA: implications for mismatch extension and lesion bypass. Mol Cell 25: 601-614.
21. Nair DT, Johnson RE, Prakash S, Prakash L, Aggarwal AK (2004) Replication by human DNA polymerase-iota occurs by Hoogsteen base-pairing. Nature 430: 377-380.
22. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2005) Human DNA Polymerase iota Incorporates dCTP Opposite Template G via a G.C+ Hoogsteen Base Pair. Structure (Camb) 13: 1569-1577.
23. Shcherbakova PV, Pavlov YI, Chilkova O, Rogozin IB, Johansson E, et al. (2003) Unique error signature of the four-subunit yeast DNA polymerase epsilon. J Biol Chem 278: 43770-43780.
24. Fortune JM, Pavlov YI, Welch CM, Johansson E, Burgers PM, et al. (2005) Saccharomyces cerevisiae DNA polymerase delta: high fidelity for base substitutions but lower fidelity for single-and multi-base deletions. J Biol Chem 280: 29980-29987.
25. Hogg M, Aller P, Konigsberg W, Wallace SS, Doublie S (2007) Structural and biochemical investigation of the role in proofreading of a beta hairpin loop found in the exonuclease domain of a replicative DNA polymerase of the B family. J Biol Chem 282: 1432-1444.
26. Reha-Krantz LJ, Marquez LA, Elisseeva E, Baker RP, Bloom LB, et al. (1998) The proofreading pathway of bacteriophage T4 DNA polymerase. J Biol Chem 273: 22969-22976.
27. Stocki SA, Nonay RL, Reha-Krantz LJ (1995) Dynamics of bacteriophage T4 DNA polymerase function: identification of amino acid residues that affect switching between polymerase and 39 -.59 exonuclease activities. J Mol Biol 254: 15-28.
28. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
29. McCoy AJ, Grosse-Kunstleve RW, Adams PD, Winn MD, Storoni LC, et al. (2007) Phaser crystallographic software. J Appl Crystallogr 40: 658-674.
30. Adams PD, Afonine PV, Bunkoczi G, Chen VB, Davis IW, et al. (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66: 213-221.
31. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
32. Chen VB, Arendall WB, 3rd, Headd JJ, Keedy DA, Immormino RM, et al. (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 66: 12-21.
33. Delano WL (2002) The PyMol Molecular Graphics System. Delano Scientific LLC, San Carlos, USA.
34. Konagurthu AS, Whisstock JC, Stuckey PJ, Lesk AM (2006) MUSTANG: a multiple structural alignment algorithm. Proteins 64: 559-574.
35. Kleywegt GJ, Jones TA (1995) Where freedom is given, liberties are taken. Structure 3: 535-540.
36. Zheng G, Lu XJ, Olson WK (2009) Web 3DNA-a web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Res 37: W240-246.