Human nucleotide excision repair protein XPA: Extended X-ray absorption fine-structure evidence for a metal-binding domain

Protein Science

Volumn 7, Issue 9, 1998, Pages 1970-1975

  Hess, Nancy J ^a   Buchko, Garry W ^a   Conradson, Steven D ^b   Espinosa, F Javier ^b   Ni, Shuisong ^a   Thrall, Brian D ^a   Kennedy, Michael A ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

DNA repair protein; EXAFS; Metalloproteins; Nucleotide excision repair; XPA

Indexed keywords

COBALT; CYSTEINE; DNA; METAL; METALLOPROTEIN; SULFUR; ZINC;

ARTICLE; CHEMICAL BOND; DNA BINDING; DNA DAMAGE; EXCISION REPAIR; HUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; X RAY ANALYSIS;

EID: 0031693584     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070912     Document Type: Article

References (52)

1. Asahina H, Kuraoka I, Shirakawa M, Morita EH, Miura N, Miyamoto I, Ohtsuka E, Okada Y, Tanaka K. 1994. The XPA protein is a zinc metalloprotein with an ability to recognize various kinds of DNA damage. Mutat Res 315:229-238.
2. Berg JM, Shi Y. 1996. The galvanization of biology. A growing appreciation of the roles of zinc. Science 271:1081-1086.
3. Bertini I, Luchinat C. 1984. High spin cobalt (II) as a probe for the investigation of metalloproteins. In: Eichorn GL, Marzilli LG, eds. Advances in inorganic biochemistry. New York: Elsevier. pp 71-111.
4. Brown GE Jr, Calas G, Waychunas GA, Petiau J. 1988. X-ray absorption spectroscopy and its applications in mineralogy and geochemistry. Rev Mineral 18:431-512.
5. 1H NMR and CD solution studies of a synthetic peptide fragment corresponding to the zinc-binding domain (101-141). J Biomol Struct Dyn 14:677-690.
6. 219). J Biomol NMR 10:313-314.
7. Buchko GW, Ni S, Thrall BD, Kennedy MA. 1998. Structural features of the minimal DNA binding domain (M98-F219) of human nucleotide excision repair protein XPA. Nucleic Acids Res 26:2779-2788.
8. Cleaver JE, Kraemer KH. 1989. Xeroderma pigmentosum and cockayne syndrome. In: Scriver SC, Beaudet AL, Sly WS, Valle D, eds. The metabolic basis of inherited disease. New York: McGraw-Hill Book Co. pp 4393-4419.
9. Coverley D, Kenny MK, Munn M, Rupp WD, Lane DP, Wood RD. 1991. Requirement for the replication protein SSB in human DNA excision repair. Nature 349:538-541.
10. Donaire A, Salgado J, Jimenez HR, Moratal JM. 1995. Cobalt substituted proteins. In: La Mer GN, ed. Nuclear magnetic resonance of paramagnetic macromolecules. The Netherlands: Kluwer Academic Publishers. pp 213-244.
11. Feiters MC, Dahlin S, Reinhammar B. 1988. The metal site of stellacyanin: EXAFS studies of the Cu(II)1 Cu(I), Ni(II) and Co(II) derivatives. Biochim Biophys Acta 955:250-260.
12. Flejter WL, McDaniel LD, Jones D, Friedberg EC, Schultz RA. 1992. Correction of xeroderma pigmentosum complementation group D mutant cell phenotypes by chromosome and gene transfer: Involvement of the human ERCC2 DNA repair gene. Proc Natl Acad Sci USA 89:261-265.
13. Frankel AD, Berg JM, Pabo CO. 1987. Metal-dependent folding of a single zinc finger from transcription factor IIIA. Proc Natl Acad Sci USA 84:4841-4845.
14. Friedberg EC, Walker GC, Siede W. 1995. DNA repair and mutagenesis. Washington, DC: American Society for Microbiology. pp 283-365.
15. Gochin M, Roder H. 1995. Protein structure refinement based on paramagnetic NMR shifts: Applications to wild-type and mutant forms of cytochrome c. Protein Sci 4:296-305.
16. Huang J-C, Svoboda DL, Reardon JT, Sancar A. 1992. Human nucleotide excision nuclease removes thymine dimers from DNA by incising the 22nd phosphodiester bond 5′ and the 5th phosphodiester bond 3′ to the photodimer. Proc Natl Acad Sci USA 89:3663-3668.
17. Jones CJ, Wood RD. 1993. Preferential binding of the xeroderma pigmentosum group A complementing protein to damaged DNA. Biochemistry 32:12096-12104.
18. Kay LE, Keifer P, Saarinen T. 1992. Pure absorption gradient enhanced heteronuclear single quantum correlated spectroscopy with improved sensitivity. J Am Chem Soc 114:10663-10665.
19. Klug A, Schwabe WR. 1995. Zinc fingers. FASEB 9:597-604.
20. Krizek BA, Merkle DL, Berg JM. 1993. Ligand variation and metal ion binding specificity in zinc finger peptides. Inorg Chem 32:937-940.
21. Kuraoka I, Morita EH, Saijo M, Matsuda T, Morikawa K, Shirakawa M, Tanaka K. 1996. Identification of a damaged-DNA binding domain of the XPA protein. Mutat Res 562:87-95.
22. Legerski R, Peterson C. 1992. Expression cloning of a human DNA repair gene involved in xeroderma pigmentosum group C. Nature 359:10-13.
23. Li L, Elledge SJ, Peterson CA, Bales ES, Legerski RJ. 1994. Specific association between the human DNA repair proteins XPA and ERCC1. Proc Natl Acad Sci USA 91:5012-5016.
24. Masutani C, Sugasawa K, Yanagisawa J, Sonoyama T, Ui M, Enomoto T, Takio K, Tanaka K, van der Spek P, Bootsma D, Hoeijmakers JHJ, Hanaoka F. 1994. Purification and cloning of a nucleotide excision repair complex involving the xeroderma pigmentosum group C protein and a human homologue of yeast RAD23. EMBO J 13:1831-1843.
25. Matsuda T, Saijo M, Kuraoka I, Kobayashi T, Nakatsu Y, Nagai A, Enjoji T, Masutani C, Sugasawa K, Hanaoka F, Yasui A, Tanaka K. 1995. DNA repair protein XPAbinds replication protein A (RPA). J Biol Chem 270:4152-4157.
26. McMaster WH, Kerr del Grande N, Mallett JH, Hubbell JH. 1969. Compilation of X-ray cross sections. Livermore: University of California. 350 pp.
27. Miyamoto I, Miura N, Niwa H, Miyazaki J, Tanaka K. 1992. Mutational analysis of the structure and function of the xeroderma pigmentosum group A complementing protein. J Biol Chem 67:12182-12187.
28. Morita EH, Ohkubo T, Kuraoko I, Shirakawa M, Tanaka K, Morikawa K. 1996. Implications of the zinc-finger motif found in the DNA-binding domain of the human XPA protein. Genes Cells 1:431-442.
29. Naegeli H. 1995. Mechanisms of DNA damage recognition in mammalian nucleotide excision repair. FASEB J 9:1043-1050.
30. Navaratnam S. Myles GM, Strange RW, Sancar A. 1989. Evidence from extended X-ray absorption fine structure and site-specific mutagenesis for zinc fingers in uvrA protein of Escherichia coli. J Biol Chem 264:16067-16071.
31. Nocentini S, Coin F, Saijo M, Tanaka K, Egly J-M. 1997. DNA damage recognition by XPA protein promotes efficient recruitment of transcription factor II H. J Biol Chem 272:22991-22994.
32. O'Donovan A, Wood RD. 1993. Identical defects in DNA repair in xeroderma pigmentosum group G and rodent ERCC group 5. Nature 363:185-188.
33. Park C-H, Mu D, Reardon JT, Sancar A. 1995. The general transcription-repair factor TFIIH is recruited to the excision repair complex by the XPA protein independent of the TFIIE transcription factor. J Biol Chem 270:4896-4901.
34. Park C-H, Sancar A. 1994. Formation of a ternary complex of human XPA, ERCC1, and ERCC4 (XPF) excision repair proteins. Proc Natl Acad Sci USA 97:5017-5021.
35. Rehr JJ, Mustre de Leon J, Zabinsky SI, Albers RC. 1991. Theoretical X-ray absorption fine structure standards. J Am Chem Soc 113:5135-5140.
36. Robins P, Jones CJ, Biggerstaff M, Lindahl T, Wood RD. 1991. Complementation of DNA repair in xeroderma pigmentosum group A cell extracts by a protein with affinity for damaged DNA. EMBO J 10:3913-12104.
37. Sancar A. 1995. DNA excision repair. J Biol Chem 270:15915-15918.
38. Satoh MS, Jones CJ, Wood RD, Lindahl T. 1993. DNA excision-repair defect of xeroderma pigmentosum prevents removal of a class of oxygen free radical-induced base lesions. Proc Natl Acad Sci USA 90:6335-6339.
39. Scherly D, Nouspikel T, Corlet J, Ucla C, Bairock A, Clarkson SG. 1993. Complementation of the DNA repair defect in xeroderma pigmentosum group G cells by a human cDNA related to yeast RAD2. Nature 363:182-185.
40. Scheuring EM, Sagi I, Chance MR. 1994. Sulfur-containing cobalmins: X-ray absorption spectroscopic characterization. Biochemistry 33:6310-6315.
41. Schmiedeskamp M, Klevit RE. 1997. Paramagnetic cobalt as a probe of the orientation of an accessory DNA-binding region of the yeast ADR1 zinc-finger protein. Biochemistry 36:14003-14011.
42. Strange RW, Murphy LM, Karlsson BG, Reinhammar B, Hasnain SS. 1996. Effect of pH and ligand binding on the structure of the Cu site of the Met121Glu mutant of azurin from Psuedomonas aeruginosa. Biochemistry 35:16391-16398.
43. Strange RW, Reinhammar B, Murphy LM, Hasnain SS. 1995. Structural and spectroscopic studies of the copper site of Stellacyanin. Biochemistry 34:220-231.
44. Summers MF, Henderson LE, Chance MR, Bess JW Jr., South TL, Blake PR, Sagi I, Perez-Alvarado G, Sowder RC III, Hare DR, Arthur LO. 1992. Nucleocapsid zinc fingers detected in retroviruses: EXAFS studies of intact viruses and the solution-state structure of the nucleocapsid protein from HIV-1. Protein Sci 1:563-574.
45. Tanaka K. 1993. Molecular analysis of xeroderma pigmentosum goup A gene. Jpn J Hum Genet 38:1-14.
46. Tanaka K, Miura N, Satokata I, Miyamoto I, Yoshida MC, Satoh Y, Kondo S, Yasui A, Okayama H, Okada Y. 1990. Analysis of a human DNA excision repair gene involved in group A xeroderma pigmentosum and containing a zinc-finger domain. Nature 348:13-16.
47. Teo BK. 1985. EXAFS: Basic principles and data analysis. Berlin: Springer-Verlag.
48. Weeda G, van Ham RCA, Vermeulen W, Bootsma D, van der Eb AJ, Hoeijmakers JHJ. 1990. A presumed DNA helicase encoded by ERCC3 is involved in the human repair disorders xeroderma pigmentosum and Cockayne's syndrome. Cell 62:777-791.
49. Wood RD. 1997. Nucleotide excision repair in mammalian cells. J Biol Chem 272:23454-23468.
50. Zabinsky SI, Rehr JJ, Ankudinov A, Albers RC, Eller MJ. 1995. Multiple scattering calculations of X-ray absorption spectra. Phys Rev B 52:2995-3010.
51. Zhang K, Auld DS. 1995. Structure of binary and ternary complexes of zinc and cobalt carboxypeptidase A as determined by X-ray absorption fine structure. Biochemistry 34:16306-16312.
52. 15N resonance assignments of the N-terminal SH3 domain of drk in folded and unfolded states using enhanced-sensitivity pulsed field gradient NMR techniques. J Biol NMR 4:845-858.