Structure of human DNA polymerase κ inserting dATP opposite an 8-OxoG DNA lesion

PLoS ONE

Volumn 4, Issue 6, 2009, Pages

  Vasquez Del Carpio, Rodrigo ^a   Silverstein, Timothy D ^a   Lone, Samer ^a   Swan, Michael K ^a   Choudhury, Jayati R ^b   Johnson, Robert E ^b   Prakash, Satya ^b   Prakash, Louise ^b   Aggarwal, Aneel K ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

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

Author keywords

[No Author keywords available]

Indexed keywords

8 HYDROXYGUANINE; DEOXYADENOSINE TRIPHOSPHATE; DNA DIRECTED DNA POLYMERASE; DNA DIRECTED DNA POLYMERASE KAPPA; UNCLASSIFIED DRUG; 7,8-DIHYDRO-8-OXOGUANINE; ADENOSINE TRIPHOSPHATE; DNA; DRUG DERIVATIVE; FREE RADICAL; GUANINE; NUCLEOTIDE; POLK PROTEIN, HUMAN;

ARTICLE; BASE PAIRING; DNA CONFORMATION; DNA DAMAGE; DNA PROTEIN COMPLEX; DNA STRUCTURE; ENZYME ACTIVE SITE; GENE INSERTION; OXIDATIVE STRESS; STRUCTURE ANALYSIS; BIOLOGICAL MODEL; CHEMISTRY; CRYSTALLIZATION; DNA REPLICATION; HUMAN; KINETICS; METABOLISM; PROTEIN CONFORMATION;

EUKARYOTA;

ADENOSINE TRIPHOSPHATE; CATALYTIC DOMAIN; CRYSTALLIZATION; DNA; DNA DAMAGE; DNA REPLICATION; DNA-DIRECTED DNA POLYMERASE; FREE RADICALS; GUANINE; HUMANS; KINETICS; MODELS, GENETIC; NUCLEOTIDES; PROTEIN CONFORMATION;

EID: 66849126006     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0005766     Document Type: Article

References (44)

1. Ames BN, Shigenaga MK, Hagen TM (1993) Oxidants, antioxidants, and the degenerative diseases of aging. Proc Natl Acad Sci U S A 90: 7915-7922.
2. Beckman KB, Ames BN (1997) Oxidative decay of DNA. J Biol Chem 272: 19633-19636.
3. Helbock HJ, Beckman KB, Shigenaga MK, Walter PB, Woodall AA, et al. (1998) DNA oxidation matters: the HPLC-electrochemical detection assay of 8-oxo-deoxyguanosine and 8-oxo-guanine. Proc Natl Acad Sci U S A 95: 288-293.
4. Prakash S, Johnson RE, Prakash L (2005) Eukaryotic Translesion Synthesis DNA Polymerases: Specificity of Structure and Function. Annu Rev Biochem 74: 317-353.
5. Johnson RE, Prakash S, Prakash L (1999) Efficient bypass of a thymine-thymine dimer by yeast DNA polymerase, Poleta. Science 283: 1001-1004.
6. Johnson RE, Washington MT, Prakash S, Prakash L (2000) Fidelity of human DNA polymerase eta. J Biol Chem 275: 7447-7450.
7. Washington MT, Johnson RE, Prakash S, Prakash L (2000) Accuracy of thymine-thymine dimer bypass by Saccharomyces cerevisiae DNA polymerase eta [see comments]. Proc Natl Acad Sci U S A 97: 3094-3099.
8. Trincao J, Johnson RE, Escalante CR, Prakash S, Prakash L, et al. (2001) Structure of the catalytic core of S. cerevisiae DNA polymerase eta: implications for translesion DNA synthesis. Mol Cell 8: 417-426.
9. Johnson RE, Kondratick CM, Prakash S, Prakash L (1999) hRAD30 mutations in the variant form of xeroderma pigmentosum [see comments]. Science 285: 263-265.
10. Masutani C, Kusumoto R, Yamada A, Dohmae N, Yokoi M, et al. (1999) The XPV (xeroderma pigmentosum variant) gene encodes human DNA polymerase eta [see comments]. Nature 399: 700-704.
11. 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.
12. Washington MT, Minko IG, Johnson RE, Wolfle WT, Harris TM, et al. (2004) Efficient and error-free replication past a minor-groove DNA adduct by the sequential action of human DNA polymerases iota and kappa. Mol Cell Biol 24: 5687-5693.
13. 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.
14. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2006) Hoogsteen base pair formation promotes synthesis opposite the 1,N6-ethenodeoxyadenosine lesion by human DNA polymerase iota. Nat Struct Mol Biol 13: 619-625.
15. Wolfle WT, Johnson RE, Minko IG, Lloyd RS, Prakash S, et al. (2006) Replication past a trans-4-hydroxynonenal minor-groove adduct by the sequential action of human DNA polymerases iota and kappa. Mol Cell Biol 26: 381-386.
16. Haracska L, Prakash S, Prakash L (2002) Yeast Rev1 protein is a G template-specific DNA polymerase. J Biol Chem 277: 15546-15551.
17. 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.
18. Nair DT, Johnson RE, Prakash L, Prakash S, Aggarwal AK (2008) Protein-template-directed synthesis across an acrolein-derived DNA adduct by yeast Rev1 DNA polymerase. Structure 16: 239-245.
19. Johnson RE, Prakash S, Prakash L (2000) The human DINB1 gene encodes the DNA polymerase Poltheta [see comments]. Proc Natl Acad Sci U S A 97: 3838-3843.
20. Ling H, Boudsocq F, Woodgate R, Yang W (2001) Crystal structure of a Y-family DNA polymerase in action: a mechanism for error-prone and lesion-bypass replication. Cell 107: 91-102.
21. Zhou BL, Pata JD, Steitz TA (2001) Crystal structure of a DinB lesion bypass DNA polymerase catalytic fragment reveals a classic polymerase catalytic domain. Mol Cell 8: 427-437.
22. Uljon SN, Johnson RE, Edwards TA, Prakash S, Prakash L, et al. (2004) Crystal structure of the catalytic core of human DNA polymerase kappa. Structure (Camb) 12: 1395-1404.
23. 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.
24. Haracska L, Yu SL, Johnson RE, Prakash L, Prakash S (2000) Efficient and accurate replication in the presence of 7,8-dihydro-8-oxoguanine by DNA polymerase eta. Nat Genet 25: 458-461.
25. Haracska L, Prakash L, Prakash S (2002) Role of human DNA polymerase kappa as an extender in translesion synthesis. Proc Natl Acad Sci U S A 99: 16000-16005.
26. Rechkoblit O, Malinina L, Cheng Y, Kuryavyi V, Broyde S, et al. (2006) Stepwise translocation of Dpo4 polymerase during error-free bypass of an oxoG lesion. PLoS Biol 4: e11.
27. Zang H, Irimia A, Choi JY, Angel KC, Loukachevitch LV, et al. (2006) Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4. J Biol Chem 281: 2358-2372.
28. 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.
29. 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.
30. Steitz TA (1999) DNA polymerases: structural diversity and common mechanisms. J Biol Chem 274: 17395-17398.
31. Shibutani S, Takeshita M, Grollman AP (1991) Insertion of specific bases during DNA synthesis past the oxidation-damaged base 8-oxodG. Nature 349: 431-434.
32. Brieba LG, Eichman BF, Kokoska RJ, Doublie S, Kunkel TA, et al. (2004) Structural basis for the dual coding potential of 8-oxoguanosine by a high-fidelity DNA polymerase. Embo J 23: 3452-3461.
33. Hsu GW, Ober M, Carell T, Beese LS (2004) Error-prone replication of oxidatively damaged DNA by a high-fidelity DNA polymerase. Nature 431: 217-221.
34. Krahn JM, Beard WA, Miller H, Grollman AP, Wilson SH (2003) Structure of DNA polymerase beta with the mutagenic DNA lesion 8-oxodeoxyguanine reveals structural insights into its coding potential. Structure 11: 121-127.
35. Freisinger E, Grollman AP, Miller H, Kisker C (2004) Lesion (in)tolerance reveals insights into DNA replication fidelity. Embo J 23: 1494-1505.
36. Washington MT, Johnson RE, Prakash L, Prakash S (2002) Human DINB1-encoded DNA polymerase kappa is a promiscuous extender of mispaired primer termini. Proc Natl Acad Sci U S A 99: 1910-1914.
37. Brieba LG, Kokoska RJ, Bebenek K, Kunkel TA, Ellenberger T (2005) A lysine residue in the fingers subdomain of T7 DNA polymerase modulates the miscoding potential of 8-oxo-7,8-dihydroguanosine. Structure 13: 1653-1659.
38. Johnson RE, Prakash L, Prakash S (2006) Yeast and human translesion DNA synthesis polymerases: expression, purification, and biochemical characterization. Methods Enzymol 408: 390-417.
39. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276: 307-326.
40. McCoy AJ, Grosse-Kunstleve RW, Storoni LC, Read RJ (2005) Likelihood-enhanced fast translation functions. Acta Crystallogr D Biol Crystallogr 61: 458-464.
41. Brunger AT, Adams PD, Clore GM, Delano WL, Gros P, et al. (1998) Crystallography & NMR system: A software suite for macromolecular structure determination. Acta Cryst D54: 905.
42. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60: 2126-2132.
43. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst A47: 110-119.
44. Delano WL (2002) The PyMol Molecular Graphics System. Delano Scientific LLC, San Carlos, USA.