PDBsum entry 1adn

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protein metals links
Transcription regulation PDB id
Protein chain
92 a.a. *
* Residue conservation analysis
PDB id:
Name: Transcription regulation
Title: Solution structure of the DNA methylphosphotriester repair domain of escherichia coli ada
Structure: N-ada 10. Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562
NMR struc: 14 models
Authors: L.C.Myers,G.L.Verdine,G.Wagner
Key ref:
L.C.Myers et al. (1993). Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada. Biochemistry, 32, 14089-14094. PubMed id: 8260490 DOI: 10.1021/bi00214a003
30-Sep-93     Release date:   31-Jan-94    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06134  (ADA_ECOLI) -  Bifunctional transcriptional activator/DNA repair enzyme Ada
354 a.a.
92 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: E.C.2.1.1  - Guanidinoacetate N-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Creatine Biosynthesis
      Reaction: S-adenosyl-L-methionine + guanidinoacetate = S-adenosyl-L-homocysteine + creatine
+ guanidinoacetate
= S-adenosyl-L-homocysteine
+ creatine
   Enzyme class 2: E.C.  - Methylated-DNA--[protein]-cysteine S-methyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: DNA (containing 6-O-methylguanine) + protein L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine
DNA (containing 6-O-methylguanine)
+ protein L-cysteine
= DNA (without 6-O-methylguanine)
+ protein S-methyl-L-cysteine
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     DNA repair   2 terms 
  Biochemical function     DNA binding     3 terms  


DOI no: 10.1021/bi00214a003 Biochemistry 32:14089-14094 (1993)
PubMed id: 8260490  
Solution structure of the DNA methyl phosphotriester repair domain of Escherichia coli Ada.
L.C.Myers, G.L.Verdine, G.Wagner.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
19920061 G.D.Jones, R.C.Le Pla, and P.B.Farmer (2010).
Phosphotriester adducts (PTEs): DNA's overlooked lesion.
  Mutagenesis, 25, 3.  
18648687 A.I.Anzellotti, and N.P.Farrell (2008).
Zinc metalloproteins as medicinal targets.
  Chem Soc Rev, 37, 1629-1651.  
18772284 A.M.Krishnakumar, D.Sliwa, J.A.Endrizzi, E.S.Boyd, S.A.Ensign, and J.W.Peters (2008).
Getting a handle on the role of coenzyme M in alkene metabolism.
  Microbiol Mol Biol Rev, 72, 445-456.  
19484137 G.Parkin (2007).
Applications of Tripodal [S(3)] and [Se(3)] L(2)X Donor Ligands to Zinc, Cadmium and Mercury Chemistry: Organometallic and Bioinorganic Perspectives.
  New J Chem, 31, 1996-2014.  
17376731 J.Penner-Hahn (2007).
Zinc-promoted alkyl transfer: a new role for zinc.
  Curr Opin Chem Biol, 11, 166-171.  
16452614 H.Takinowaki, Y.Matsuda, T.Yoshida, Y.Kobayashi, and T.Ohkubo (2006).
The solution structure of the methylated form of the N-terminal 16-kDa domain of Escherichia coli Ada protein.
  Protein Sci, 15, 487-497.
PDB code: 1wpk
16464003 Y.Mishina, E.M.Duguid, and C.He (2006).
Direct reversal of DNA alkylation damage.
  Chem Rev, 106, 215-232.  
16240665 W.Maret (2005).
Zinc coordination environments in proteins determine zinc functions.
  J Trace Elem Med Biol, 19, 7.  
12524213 S.A.Ensign, and J.R.Allen (2003).
Aliphatic epoxide carboxylation.
  Annu Rev Biochem, 72, 55-76.  
12527760 S.S.Krishna, I.Majumdar, and N.V.Grishin (2003).
Structural classification of zinc fingers: survey and summary.
  Nucleic Acids Res, 31, 532-550.  
11939797 J.G.Krum, H.Ellsworth, R.R.Sargeant, G.Rich, and S.A.Ensign (2002).
Kinetic and microcalorimetric analysis of substrate and cofactor interactions in epoxyalkane:CoM transferase, a zinc-dependent epoxidase.
  Biochemistry, 41, 5005-5014.  
11352719 S.A.Ensign (2001).
Microbial metabolism of aliphatic alkenes.
  Biochemistry, 40, 5845-5853.  
11439187 Z.J.Sun, K.S.Kim, G.Wagner, and E.L.Reinherz (2001).
Mechanisms contributing to T cell receptor signaling and assembly revealed by the solution structure of an ectodomain fragment of the CD3 epsilon gamma heterodimer.
  Cell, 105, 913-923.
PDB code: 1jbj
10704208 C.Huang, K.E.Hightower, and C.A.Fierke (2000).
Mechanistic studies of rat protein farnesyltransferase indicate an associative transition state.
  Biochemistry, 39, 2593-2602.  
10785368 K.Sauer, and R.K.Thauer (2000).
Methyl-coenzyme M formation in methanogenic archaea. Involvement of zinc in coenzyme M activation.
  Eur J Biochem, 267, 2498-2504.  
10226042 K.E.Hightower, and C.A.Fierke (1999).
Zinc-catalyzed sulfur alkyation:insights from protein farnesyltransferase.
  Curr Opin Chem Biol, 3, 176-181.  
10625458 Z.S.Zhou, K.Peariso, J.E.Penner-Hahn, and R.G.Matthews (1999).
Identification of the zinc ligands in cobalamin-independent methionine synthase (MetE) from Escherichia coli.
  Biochemistry, 38, 15915-15926.  
9799520 K.E.Hightower, C.C.Huang, P.J.Casey, and C.A.Fierke (1998).
H-Ras peptide and protein substrates bind protein farnesyltransferase as an ionized thiolate.
  Biochemistry, 37, 15555-15562.  
  9098899 D.L.Pountney, R.P.Tiwari, and J.B.Egan (1997).
Metal- and DNA-binding properties and mutational analysis of the transcription activating factor, B, of coliphage 186: a prokaryotic C4 zinc-finger protein.
  Protein Sci, 6, 892-902.  
9667865 R.G.Matthews, and C.W.Goulding (1997).
Enzyme-catalyzed methyl transfers to thiols: the role of zinc.
  Curr Opin Chem Biol, 1, 332-339.  
8702528 G.M.LeClerc, and D.A.Grahame (1996).
Methylcobamide:coenzyme M methyltransferase isozymes from Methanosarcina barkeri. Physicochemical characterization, cloning, sequence analysis, and heterologous gene expression.
  J Biol Chem, 271, 18725-18731.  
8755711 J.Habazettl, L.C.Myers, F.Yuan, G.L.Verdine, and G.Wagner (1996).
Backbone dynamics, amide hydrogen exchange, and resonance assignments of the DNA methylphosphotriester repair domain of Escherichia coli Ada using NMR.
  Biochemistry, 35, 9335-9348.  
7773744 J.A.Tainer, M.M.Thayer, and R.P.Cunningham (1995).
DNA repair proteins.
  Curr Opin Struct Biol, 5, 20-26.  
7896807 L.C.Myers, F.Jackow, and G.L.Verdine (1995).
Metal dependence of transcriptional switching in Escherichia coli Ada.
  J Biol Chem, 270, 6664-6670.  
8533156 L.H.Pearl, and R.Savva (1995).
DNA repair in three dimensions.
  Trends Biochem Sci, 20, 421-426.  
8293456 G.L.Verdine (1994).
The flip side of DNA methylation.
  Cell, 76, 197-200.  
9383376 L.C.Myers, T.D.Cushing, G.Wagner, and G.L.Verdine (1994).
Metal-coordination sphere in the methylated Ada protein-DNA co-complex.
  Chem Biol, 1, 91-97.  
8065896 L.Szilák, C.Finta, A.Patthy, P.Venetianer, and A.Kiss (1994).
Self-methylation of BspRI DNA-methyltransferase.
  Nucleic Acids Res, 22, 2876-2881.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.