1adn Citations

Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada.

Biochemistry 32 14089-94 (1993)
Cited: 41 times
EuropePMC logo PMID: 8260490

Abstract

The Escherichia coli Ada protein repairs methyl phosphotriesters in DNA by direct, irreversible methyl transfer to one of its own cysteine residues. The methyl-transfer process appears to be autocatalyzed by coordination of the acceptor residue, Cys-69, to a tightly bound zinc ion. Upon methyl transfer, Ada acquires the ability to bind DNA sequence-specifically and thereby to induce genes that confer resistance to methylating agents. The solution structure of an N-terminal 10-kDa fragment of Ada, which retains zinc binding and DNA methyl phosphotriester repair activities, was determined using multidimensional heteronuclear nuclear magnetic resonance techniques. The structure reveals a zinc-binding motif unlike any observed thus far in transcription factors or zinc-containing enzymes and provides insight into the mechanism of metalloactivated DNA repair.

Articles - 1adn mentioned but not cited (1)



Reviews citing this publication (22)

  1. Direct reversal of DNA alkylation damage. Mishina Y, Duguid EM, He C. Chem. Rev. 106 215-232 (2006)
  2. Multifaceted roles of alkyltransferase and related proteins in DNA repair, DNA damage, resistance to chemotherapy, and research tools. Pegg AE. Chem. Res. Toxicol. 24 618-639 (2011)
  3. Enzyme-catalyzed methyl transfers to thiols: the role of zinc. Matthews RG, Goulding CW. Curr Opin Chem Biol 1 332-339 (1997)
  4. Zinc coordination environments in proteins determine zinc functions. Maret W. J Trace Elem Med Biol 19 7-12 (2005)
  5. The flip side of DNA methylation. Verdine GL. Cell 76 197-200 (1994)
  6. Zinc metalloproteins as medicinal targets. Anzellotti AI, Farrell NP. Chem Soc Rev 37 1629-1651 (2008)
  7. Zinc-catalyzed sulfur alkyation:insights from protein farnesyltransferase. Hightower KE, Fierke CA. Curr Opin Chem Biol 3 176-181 (1999)
  8. DNA damage-induced gene expression in Saccharomyces cerevisiae. Fu Y, Pastushok L, Xiao W. FEMS Microbiol. Rev. 32 908-926 (2008)
  9. Aliphatic epoxide carboxylation. Ensign SA, Allen JR. Annu. Rev. Biochem. 72 55-76 (2003)
  10. DNA repair proteins. Tainer JA, Thayer MM, Cunningham RP. Curr. Opin. Struct. Biol. 5 20-26 (1995)
  11. DNA repair in three dimensions. Pearl LH, Savva R. Trends Biochem. Sci. 20 421-426 (1995)
  12. Multifaceted roles of alkyltransferase and related proteins in DNA repair, DNA damage, resistance to chemotherapy, and research tools. Pegg AE. Chem. Res. Toxicol. 24 618-639 (2011)
  13. DNA damage-induced gene expression in Saccharomyces cerevisiae. Fu Y, Pastushok L, Xiao W. FEMS Microbiol. Rev. 32 908-926 (2008)
  14. Zinc metalloproteins as medicinal targets. Anzellotti AI, Farrell NP. Chem Soc Rev 37 1629-1651 (2008)
  15. Direct reversal of DNA alkylation damage. Mishina Y, Duguid EM, He C. Chem. Rev. 106 215-232 (2006)
  16. Zinc coordination environments in proteins determine zinc functions. Maret W. J Trace Elem Med Biol 19 7-12 (2005)
  17. Aliphatic epoxide carboxylation. Ensign SA, Allen JR. Annu. Rev. Biochem. 72 55-76 (2003)
  18. Zinc-catalyzed sulfur alkyation:insights from protein farnesyltransferase. Hightower KE, Fierke CA. Curr Opin Chem Biol 3 176-181 (1999)
  19. Enzyme-catalyzed methyl transfers to thiols: the role of zinc. Matthews RG, Goulding CW. Curr Opin Chem Biol 1 332-339 (1997)
  20. DNA repair proteins. Tainer JA, Thayer MM, Cunningham RP. Curr. Opin. Struct. Biol. 5 20-26 (1995)
  21. DNA repair in three dimensions. Pearl LH, Savva R. Trends Biochem. Sci. 20 421-426 (1995)
  22. The flip side of DNA methylation. Verdine GL. Cell 76 197-200 (1994)

Articles citing this publication (18)

  1. Structural classification of zinc fingers: survey and summary. Krishna SS, Majumdar I, Grishin NV. Nucleic Acids Res. 31 532-550 (2003)
  2. Mechanisms contributing to T cell receptor signaling and assembly revealed by the solution structure of an ectodomain fragment of the CD3 epsilon gamma heterodimer. Sun ZJ, Kim KS, Wagner G, Reinherz EL. Cell 105 913-923 (2001)
  3. Minimal functional sites allow a classification of zinc sites in proteins. Andreini C, Bertini I, Cavallaro G. PLoS ONE 6 e26325 (2011)
  4. Zinc-promoted alkyl transfer: a new role for zinc. Penner-Hahn J. Curr Opin Chem Biol 11 166-171 (2007)
  5. Metal- and DNA-binding properties and mutational analysis of the transcription activating factor, B, of coliphage 186: a prokaryotic C4 zinc-finger protein. Pountney DL, Tiwari RP, Egan JB. Protein Sci. 6 892-902 (1997)
  6. Trapping distinct structural states of a protein/DNA interaction through disulfide crosslinking. He C, Verdine GL. Chem. Biol. 9 1297-1303 (2002)
  7. Methyl-coenzyme M formation in methanogenic archaea. Involvement of zinc in coenzyme M activation. Sauer K, Thauer RK. Eur. J. Biochem. 267 2498-2504 (2000)
  8. Applications of Tripodal [S(3)] and [Se(3)] L(2)X Donor Ligands to Zinc, Cadmium and Mercury Chemistry: Organometallic and Bioinorganic Perspectives. Parkin G. New J Chem 31 1996-2014 (2007)
  9. The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein. Takinowaki H, Matsuda Y, Yoshida T, Kobayashi Y, Ohkubo T. Protein Sci. 15 487-497 (2006)
  10. Metal-coordination sphere in the methylated Ada protein-DNA co-complex. Myers LC, Cushing TD, Wagner G, Verdine GL. Chem. Biol. 1 91-97 (1994)
  11. Self-methylation of BspRI DNA-methyltransferase. Szilák L, Finta C, Patthy A, Venetianer P, Kiss A. Nucleic Acids Res. 22 2876-2881 (1994)
  12. The chemical and biochemical properties of methylphosphotriester DNA. Buck HM. Nucleosides Nucleotides Nucleic Acids 23 1833-1847 (2004)
  13. Direct measurements of the mechanical stability of zinc-thiolate bonds in rubredoxin by single-molecule atomic force microscopy. Zheng P, Li H. Biophys. J. 101 1467-1473 (2011)
  14. On the design of zinc-finger models with cyclic peptides bearing a linear tail. Jacques A, Mettra B, Lebrun V, Latour JM, Sénèque O. Chemistry 19 3921-3931 (2013)
  15. Oxidation of Zn(Cys)4 zinc finger peptides by O2 and H2O2: products, mechanism and kinetics. Bourlès E, Isaac M, Lebrun C, Latour JM, Sénèque O. Chemistry 17 13762-13772 (2011)
  16. The molecular structure of the tris(2-mercapto-1-tolylimidazolyl)hydroborato zinc(2-mercapto-1-tolylimidazole) complex, [[Tm(p-Tol)]Zn(mim(p-Tol))][ClO4]: intermolecular N-H...OClO3versus intramolecular N-H...S hydrogen bonding interactions of the mercaptoimidazole ligand. Morlok MM, Docrat A, Janak KE, Tanski JM, Parkin G. Dalton Trans 3448-3452 (2004)
  17. Spectroscopic, electrochemical, and alkylation reactions: tert-butyl N-(2-mercaptoethyl)carbamate copper(II) and nickel(II) complexes as structural mimics for the active site of thiolate-alkylating enzymes. Ibrahim MM, Mersal GA, El-Shafai N, Ramadan AM, Youssef MM. Spectrochim Acta A Mol Biomol Spectrosc 120 574-584 (2014)
  18. Classification of the treble clef zinc finger: noteworthy lessons for structure and function evolution. Kaur G, Subramanian S. Sci Rep 6 32070 (2016)


Related citations provided by authors (1)

  1. Repair of DNA Methylphosphotriesters Through a Metalloactivated Cysteine Nucleophile. Myers LC, Terranova MP, Ferentz AE, Wagner G, Verdine GL Science 261 1164- (1993)