Article

You have full text access to this OnlineOpen article

Involvement of a carboxylated lysine in UV damage endonuclease

  1. Elisabeth M. Meulenbroek1,2,
  2. Keti Paspaleva2,
  3. Ellen A. J. Thomassen1,
  4. Jan Pieter Abrahams1,
  5. Nora Goosen2,*,
  6. Navraj S. Pannu1,*

Article first published online: 6 JAN 2009

DOI: 10.1002/pro.54

Issue

Protein Science

Protein Science

Volume 18, Issue 3, pages 549–558, March 2009

Additional Information

How to Cite

Meulenbroek, E. M., Paspaleva, K., Thomassen, E. A. J., Abrahams, J. P., Goosen, N. and Pannu, N. S. (2009), Involvement of a carboxylated lysine in UV damage endonuclease. Protein Science, 18: 549–558. doi: 10.1002/pro.54

Author Information

  1. 1

    Biophysical Structural Chemistry, Leiden Institute of Chemistry, 2300 RA Leiden, The Netherlands

  2. 2

    Laboratory of Molecular Genetics, Leiden Institute of Chemistry, 2300 RA Leiden, The Netherlands

*Laboratory of Molecular Genetics, Leiden Institute of Chemistry, P.O. Box 9502, 2300 RA Leiden, The Netherlands

Publication History

  1. Issue published online: 23 FEB 2009
  2. Article first published online: 6 JAN 2009
  3. Accepted manuscript online: 6 JAN 2009 12:00AM EST
  4. Manuscript Accepted: 1 DEC 2008
  5. Manuscript Revised: 25 NOV 2008
  6. Manuscript Received: 18 SEP 2008

SEARCH

SEARCH BY CITATION

ARTICLE TOOLS

View Full Article (HTML) Get PDF (502K)

References

  • 1
    Sidik K, Lieberman HB, Freyer GA ( 1992) Repair of DNA damaged by UV-light and ionizing-radiation by cell-free-extracts prepared from Schizosaccharomyces pombe. Proc Natl Acad Sci USA 89: 1212–1216.
  • 2
    Bowman KK, Sidik K, Smith CA, Taylor JS, Doetsch PW, Freyer GA ( 1994) A new ATP-independent DNA endonuclease from Schizosaccharomyces pombe that recognizes cyclobutane pyrimidine dimers and 6-4-photoproducts. Nucleic Acids Res 22: 3026–3032.
  • 3
    Avery AM, Kaur B, Taylor J, Mello JA, Essigmann JM, Doetsch PW ( 1999) Substrate specificity of ultraviolet DNA endonuclease (UVDE/Uve1p) from Schizosaccharomyces pombe. Nucleic Acids Res 27: 2256–2264.
  • 4
    Paspaleva K, Thomassen E, Pannu NS, Iwai S, Moolenaar GF, Goosen N, Abrahams JP ( 2007) Crystal structure of the DNA repair enzyme UV damage endonuclease. Structure 15: 1316–1324.
  • 5
    Abendroth J, Niefind K, Schomburg D ( 2002) X-ray structure of a dihydropyrimidinase from Thermus sp. at 1.3 Angstrom resolution. J Mol Biol 320: 143–156.
  • 6
    Cha J, Mobashery S ( 2007) Lysine N-zeta-decarboxylation in the BlaR1 protein from Staphylococcus aureus at the root of its function as an antibiotic sensor. J Am Chem Soc 129: 3834–3835.
  • 7
    Golema-Kotra D, Cha JY, Meroueh SO, Vakulenko SB, Mobashery S ( 2003) Resistance of beta-lactam antibiotics and its mediation by the sensor domain of the transmembrane BlaR signalling pathway in Staphylococcus aureus. J Biol Chem 278: 18419–18425.
  • 8
    Golemi D, Maveyraud L, Vakulenko S, Samama J, Mobashery S ( 2001) Critical involvement of a carbamylated lysine in catalytic function of class D beta-lactamases. Proc Natl Acad Sci USA 98: 14280–14285.
  • 9
    Li J, Cross JB, Vreven T, Meroueh SO, Schlegel HB ( 2005) Lysine carboxylation in proteins: OXA-10 beta-lactamase. Proteins 61: 246–257.
    Direct Link:
  • 10
    Thoden JB, Philips GN, Neal TM, Raushel FM, Holden HM ( 2001) Molecular structure of dihydroorotase: a paradigm for catalysis through the use of a binuclear metal center. Biochem 40: 6989–6997.
  • 11
    Thoden JB, Marti-Arbona R, Raushel FM, Holden HM ( 2003) High-resolution X-ray structure of isoaspartyl dipeptidase from Escherichia coli. Biochemistry 42: 4874–4882.
  • 12
    Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA ( 1999) Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98: 397–408.
  • 13
    Weiss MS, Hilgenfeld R ( 1997) On the use of the merging R factor as a quality indicator for X-ray data. J Appl Cryst 30: 203–205.
    Direct Link:
  • 14
    Diederichs K, Karplus PA ( 1997) Improved R-factors for diffraction data analysis in macromolecular crystallography. Nat Struct Biol 4: 269–275.
  • 15
    Laskowski RA, MacAuthor MW, Moss DS, Thornton JM ( 1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26: 283–291.
    Direct Link:
  • 16
    Murshudov GN, Vagin AA, Dodson EJ ( 1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst D 50: 760–763.
  • 17
    Goosen N, Moolenaar GF ( 2008) Repair of UV damage in bacteria. DNA repair 7: 353–379.
  • 18
    Iwai S ( 2006) Chemical synthesis of oligonucleotides containing damaged bases for biological studies. Nucleosides Nucleotides Nucleic Acids 25: 561–582.
  • 19
    Verhoeven EE, Van Kesteren M, Turner JJ, Van der Maarel GA, Van Boom JH, Moolenaar GF, Goosen N ( 2002) The C-terminal region of Escherichia coli UvrC contributes to the flexibility of the UvrABC nucleotide excision repair system. Nucleic Acids Res 30: 2492–2500.
  • 20
    Popov AN, Bourenkov GP ( 2003) Choice of data-collection parameters based on statistical modelling. Acta Cryst D 59: 1145–1153.
    Direct Link:
  • 21
    Leslie AG ( 1999) Integration of macromolecular diffraction data. Acta Cryst D 55: 1696–1702.
    Direct Link:
  • 22
    Collaborative Computational Project 4 ( 1994) The CCP4 suite: programs for protein crystallography. Acta Cryst D 50: 760–763.
    Direct Link:
  • 23
    Vagin A, Teplyakov A ( 1997) MOLREP: an automated program for molecular replacement. J Appl Cryst 30: 1022–1025.
    Direct Link:
  • 24
    Emsley P, Cowtan K ( 2004) Coot: model-building tools for molecular graphics. Acta Cryst D 60: 2126–2132.
    Direct Link:
  • 25
    Perrakis A, Morris R, Lamzin VS ( 1999) Automated protein model building combined with iterative structure refinement. Nat Struct Biol 6: 458–463.
  • 26
    Potterton L, McNicholas S, Krissinel E, Gruber J, Cowtan K, Emsley P, Murshudov GN, Cohen S, Perrakis A, Noble M ( 2004) Developments in the CCP4 molecular graphics project. Acta Cryst D 60: 2288–2294.
    Direct Link:
View Full Article (HTML) Get PDF (502K)