1EYF

REFINED STRUCTURE OF THE DNA METHYL PHOSPHOTRIESTER REPAIR DOMAIN OF E. COLI ADA

Summary for 1EYF

• Entry DOI: 10.2210/pdb1eyf/pdb
• Related: 1ADN
• NMR Information: BMRB: 4925
• Descriptor: ADA REGULATORY PROTEIN, ZINC ION (2 entities in total)
• Functional Keywords: one central beta-sheet sandwiched between two alpha-helices, dna binding protein
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 10535.39

Authors

Lin, Y.,Dotsch, V.,Wintner, T.,Peariso, K.,Myers, L.C.,Penner-Hahn, J.E.,Verdine, G.L.,Wagner, G. (deposition date: 2000-05-06, release date: 2003-09-09, Last modification date: 2024-05-22)

Primary citation

Lin, Y.,Dotsch, V.,Wintner, T.,Peariso, K.,Myers, L.C.,Penner-Hahn, J.E.,Verdine, G.L.,Wagner, G.
Structural basis for the functional switch of the E. coli Ada protein
Biochemistry, 40:4261-4271, 2001

PubMed Abstract: The Escherichia coli protein Ada specifically repairs the S(p) diastereomer of DNA methyl phosphotriesters in DNA by direct and irreversible transfer of the methyl group to its own Cys 69 which is part of a zinc-thiolate center. The methyl transfer converts Ada into a transcriptional activator that binds sequence-specifically to promoter regions of its own gene and other methylation resistance genes. Ada thus acts as a chemosensor to activate repair mechanisms in situations of methylation damage. Here we present a highly refined solution structure of the 10 kDa N-terminal domain, N-Ada10, which reveals structural details of the nonspecific DNA interaction of N-Ada10 during the repair process and provides a basis for understanding the mechanism of the conformational switch triggered by methyl transfer. To further elucidate this, EXAFS (extended X-ray absorption fine structure) and XANES (X-ray absorption near-edge structure) data were acquired, which confirmed that the zinc-thiolate center is maintained when N-Ada is methylated. Thus, ligand exchange is not the mechanism that enhances sequence-specific DNA binding and transcriptional activation upon methylation of N-Ada. The mechanism of the switch was further elucidated by recording NOESY spectra of specifically labeled methylated-Ada/DNA complexes, which showed that the transferred methyl group makes many contacts within N-Ada but none with the DNA. This implies that methylation of N-Ada induces a structural change, which enhances the promoter affinity of a remodeled surface region that does not include the transferred methyl group.

PubMed: 11284682
DOI: 10.1021/bi002109p

Experimental method

SOLUTION NMR