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PDBsum entry 1sfe

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protein links
DNA-binding protein PDB id
1sfe
Jmol
Contents
Protein chain
165 a.a. *
Waters ×145
* Residue conservation analysis
PDB id:
1sfe
Name: DNA-binding protein
Title: Ada o6-methylguanine-DNA methyltransferase from escherichia
Structure: Ada o6-methylguanine-DNA methyltransferase. Chain: a. Fragment: c-terminal 19kd of the ada protein. Engineered: yes
Source: Escherichia coli. Organism_taxid: 37762. Strain: b. Variant: jm 101. Gene: adac. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: tac control
Resolution:
2.10Å     R-factor:   0.219    
Authors: M.H.Moore,J.M.Gulbis,E.J.Dodson,B.Demple,P.C.E.Moody
Key ref: M.H.Moore et al. (1994). Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli. EMBO J, 13, 1495-1501. PubMed id: 8156986
Date:
21-Jun-96     Release date:   23-Dec-96    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P06134  (ADA_ECOLI) -  Bifunctional transcriptional activator/DNA repair enzyme Ada
Seq:
Struc:
354 a.a.
165 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

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

      Pathway:
Creatine Biosynthesis
      Reaction: S-adenosyl-L-methionine + guanidinoacetate = S-adenosyl-L-homocysteine + creatine
S-adenosyl-L-methionine
+ guanidinoacetate
= S-adenosyl-L-homocysteine
+ creatine
   Enzyme class 2: E.C.2.1.1.63  - 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   1 term 
  Biochemical function     catalytic activity     2 terms  

 

 
    reference    
 
 
EMBO J 13:1495-1501 (1994)
PubMed id: 8156986  
 
 
Crystal structure of a suicidal DNA repair protein: the Ada O6-methylguanine-DNA methyltransferase from E. coli.
M.H.Moore, J.M.Gulbis, E.J.Dodson, B.Demple, P.C.Moody.
 
  ABSTRACT  
 
The mutagenic and carcinogenic effects of simple alkylating agents are mainly due to methylation at the O6 position of guanine in DNA. O6-methylguanine directs the incorporation of either thymine or cytosine without blocking DNA replication, resulting in GC to AT transition mutations. In prokaryotic and eukaryotic cells antimutagenic repair is effected by direct reversal of this DNA damage. A suicidal methyltransferase repair protein removes the methyl group from DNA to one of its own cysteine residues. The resulting self-methylation of the active site cysteine renders the protein inactive. Here we report the X-ray structure of the 19 kDa C-terminal domain of the Escherichia coli ada gene product, the prototype of these suicidal methyltransferases. In the crystal structure the active site cysteine is buried. We propose a model for the significant conformational change that the protein must undergo in order to bind DNA and effect methyl transfer.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20717836 B.Kaina, G.P.Margison, and M.Christmann (2010).
Targeting O⁶-methylguanine-DNA methyltransferase with specific inhibitors as a strategy in cancer therapy.
  Cell Mol Life Sci, 67, 3663-3681.  
21192796 K.F.Kong, A.Aguila, L.Schneper, and K.Mathee (2010).
Pseudomonas aeruginosa β-lactamase induction requires two permeases, AmpG and AmpP.
  BMC Microbiol, 10, 328.  
20026607 Q.Fang, S.Kanugula, J.L.Tubbs, J.A.Tainer, and A.E.Pegg (2010).
Repair of O4-alkylthymine by O6-alkylguanine-DNA alkyltransferases.
  J Biol Chem, 285, 8185-8195.  
19542005 N.P.Khairnar, and H.S.Misra (2009).
DNA polymerase X from Deinococcus radiodurans implicated in bacterial tolerance to DNA damage is characterized as a short patch base excision repair polymerase.
  Microbiology, 155, 3005-3014.  
19254550 Y.Lin, T.Zhao, X.Jian, Z.Farooqui, X.Qu, C.He, A.R.Dinner, and N.F.Scherer (2009).
Using the bias from flow to elucidate single DNA repair protein sliding and interactions with DNA.
  Biophys J, 96, 1911-1917.  
18803403 Q.Fang, A.M.Noronha, S.P.Murphy, C.J.Wilds, J.L.Tubbs, J.A.Tainer, G.Chowdhury, F.P.Guengerich, and A.E.Pegg (2008).
Repair of O6-G-alkyl-O6-G interstrand cross-links by human O6-alkylguanine-DNA alkyltransferase.
  Biochemistry, 47, 10892-10903.  
17485252 J.L.Tubbs, A.E.Pegg, and J.A.Tainer (2007).
DNA binding, nucleotide flipping, and the helix-turn-helix motif in base repair by O6-alkylguanine-DNA alkyltransferase and its implications for cancer chemotherapy.
  DNA Repair (Amst), 6, 1100-1115.  
16826543 A.Roberts, J.G.Pelton, and D.E.Wemmer (2006).
Structural studies of MJ1529, an O6-methylguanine-DNA methyltransferase.
  Magn Reson Chem, 44, S71-S82.
PDB code: 2g7h
16698182 C.A.Rabik, M.C.Njoku, and M.E.Dolan (2006).
Inactivation of O6-alkylguanine DNA alkyltransferase as a means to enhance chemotherapy.
  Cancer Treat Rev, 32, 261-276.  
16464003 Y.Mishina, E.M.Duguid, and C.He (2006).
Direct reversal of DNA alkylation damage.
  Chem Rev, 106, 215-232.  
15808743 L.Aravind, V.Anantharaman, S.Balaji, M.M.Babu, and L.M.Iyer (2005).
The many faces of the helix-turn-helix domain: transcription regulation and beyond.
  FEMS Microbiol Rev, 29, 231-262.  
15972855 M.A.Calmann, J.E.Evans, and M.G.Marinus (2005).
MutS inhibits RecA-mediated strand transfer with methylated DNA substrates.
  Nucleic Acids Res, 33, 3591-3597.  
15731349 S.Kanugula, G.T.Pauly, R.C.Moschel, and A.E.Pegg (2005).
A bifunctional DNA repair protein from Ferroplasma acidarmanus exhibits O6-alkylguanine-DNA alkyltransferase and endonuclease V activities.
  Proc Natl Acad Sci U S A, 102, 3617-3622.  
15040447 B.Sedgwick (2004).
Repairing DNA-methylation damage.
  Nat Rev Mol Cell Biol, 5, 148-157.  
14691244 J.J.Rasimas, P.A.Dalessio, I.J.Ropson, A.E.Pegg, and M.G.Fried (2004).
Active-site alkylation destabilizes human O6-alkylguanine DNA alkyltransferase.
  Protein Sci, 13, 301-305.  
15057289 S.L.Gerson (2004).
MGMT: its role in cancer aetiology and cancer therapeutics.
  Nat Rev Cancer, 4, 296-307.  
14522053 E.M.Duguid, Y.Mishina, and C.He (2003).
How do DNA repair proteins locate potential base lesions? a chemical crosslinking method to investigate O6-alkylguanine-DNA alkyltransferases.
  Chem Biol, 10, 827-835.  
12496275 J.J.Rasimas, A.E.Pegg, and M.G.Fried (2003).
DNA-binding mechanism of O6-alkylguanine-DNA alkyltransferase. Effects of protein and DNA alkylation on complex stability.
  J Biol Chem, 278, 7973-7980.  
12112867 T.Imanaka, and H.Atomi (2002).
Catalyzing "hot" reactions: enzymes from hyperthermophilic Archaea.
  Chem Rec, 2, 149-163.  
11732917 J.C.Delaney, and J.M.Essigmann (2001).
Effect of sequence context on O(6)-methylguanine repair and replication in vivo.
  Biochemistry, 40, 14968-14975.  
11567157 K.Cowtan (2001).
Fast Fourier feature recognition.
  Acta Crystallogr D Biol Crystallogr, 57, 1435-1444.  
11488906 K.Shiraki, S.Nishikori, S.Fujiwara, H.Hashimoto, Y.Kai, M.Takagi, and T.Imanaka (2001).
Comparative analyses of the conformational stability of a hyperthermophilic protein and its mesophilic counterpart.
  Eur J Biochem, 268, 4144-4150.  
11746760 S.Kanugula, and A.E.Pegg (2001).
Novel DNA repair alkyltransferase from Caenorhabditis elegans.
  Environ Mol Mutagen, 38, 235-243.  
10747039 D.S.Daniels, C.D.Mol, A.S.Arvai, S.Kanugula, A.E.Pegg, and J.A.Tainer (2000).
Active and alkylated human AGT structures: a novel zinc site, inhibitor and extrahelical base binding.
  EMBO J, 19, 1719-1730.
PDB codes: 1eh6 1eh7 1eh8
10606635 J.E.Wibley, A.E.Pegg, and P.C.Moody (2000).
Crystal structure of the human O(6)-alkylguanine-DNA alkyltransferase.
  Nucleic Acids Res, 28, 393-401.
PDB code: 1qnt
10677686 L.R.Brown, J.Deng, and N.D.Clarke (2000).
Dominant sensitization variants of human O(6)-methylguanine-DNA-methyltransferase obtained by a mutational screen of surface residues.
  Mutat Res, 459, 81-87.  
11000262 P.E.Verdemato, J.A.Brannigan, C.Damblon, F.Zuccotto, P.C.Moody, and L.Y.Lian (2000).
DNA-binding mechanism of the Escherichia coli Ada O(6)-alkylguanine-DNA alkyltransferase.
  Nucleic Acids Res, 28, 3710-3718.  
11073893 P.Landini, and M.R.Volkert (2000).
Regulatory responses of the adaptive response to alkylation damage: a simple regulon with complex regulatory features.
  J Bacteriol, 182, 6543-6549.  
10584923 B.M.Davis, J.C.Roth, L.Liu, M.Xu-Welliver, A.E.Pegg, and S.L.Gerson (1999).
Characterization of the P140K, PVP(138-140)MLK, and G156A O6-methylguanine-DNA methyltransferase mutants: implications for drug resistance gene therapy.
  Hum Gene Ther, 10, 2769-2778.  
10346901 T.E.Spratt, J.D.Wu, D.E.Levy, S.Kanugula, and A.E.Pegg (1999).
Reaction and binding of oligodeoxynucleotides containing analogues of O6-methylguanine with wild-type and mutant human O6-alkylguanine-DNA alkyltransferase.
  Biochemistry, 38, 6801-6806.  
10583946 T.Lindahl, and R.D.Wood (1999).
Quality control by DNA repair.
  Science, 286, 1897-1905.  
9556560 A.E.Pegg, S.Kanugula, S.Edara, G.T.Pauly, R.C.Moschel, and K.Goodtzova (1998).
Reaction of O6-benzylguanine-resistant mutants of human O6-alkylguanine-DNA alkyltransferase with O6-benzylguanine in oligodeoxyribonucleotides.
  J Biol Chem, 273, 10863-10867.  
9461471 B.Holz, S.Klimasauskas, S.Serva, and E.Weinhold (1998).
2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases.
  Nucleic Acids Res, 26, 1076-1083.  
9484244 D.Bhattacharyya, T.K.Hazra, W.D.Behnke, P.L.Chong, A.Kurosky, J.C.Lee, and S.Mitra (1998).
Reversible folding of Ada protein (O6-methylguanine-DNA methyltransferase) of Escherichia coli.
  Biochemistry, 37, 1722-1730.  
9421528 D.L.Wong, J.G.Pavlovich, and N.O.Reich (1998).
Electrospray ionization mass spectrometric characterization of photocrosslinked DNA-EcoRI DNA methyltransferase complexes.
  Nucleic Acids Res, 26, 645-649.  
10089516 H.Hashimoto, M.Nishioka, T.Inoue, S.Fujiwara, M.Takagi, T.Imanaka, and Y.Kai (1998).
Crystallization and preliminary X-ray crystallographic analysis of archaeal O6-methylguanine-DNA methyltransferase.
  Acta Crystallogr D Biol Crystallogr, 54, 1395-1396.  
9730821 K.Goodtzova, S.Kanugula, S.Edara, and A.E.Pegg (1998).
Investigation of the role of tyrosine-114 in the activity of human O6-alkylguanine-DNA alkyltranferase.
  Biochemistry, 37, 12489-12495.  
9759487 R.J.Roberts, and X.Cheng (1998).
Base flipping.
  Annu Rev Biochem, 67, 181-198.  
9032058 D.G.Vassylyev, and K.Morikawa (1997).
DNA-repair enzymes.
  Curr Opin Struct Biol, 7, 103-109.  
9079656 K.Goodtzova, S.Kanugula, S.Edara, G.T.Pauly, R.C.Moschel, and A.E.Pegg (1997).
Repair of O6-benzylguanine by the Escherichia coli Ada and Ogt and the human O6-alkylguanine-DNA alkyltransferases.
  J Biol Chem, 272, 8332-8339.  
9352585 R.O.Pieper (1997).
Understanding and manipulating O6-methylguanine-DNA methyltransferase expression.
  Pharmacol Ther, 74, 285-297.  
9354758 R.S.Lloyd, and X.Cheng (1997).
Mechanistic link between DNA methyltransferases and DNA repair enzymes by base flipping.
  Biopolymers, 44, 139-151.  
8995288 S.Cal, and B.A.Connolly (1997).
DNA distortion and base flipping by the EcoRV DNA methyltransferase. A study using interference at dA and T bases and modified deoxynucleosides.
  J Biol Chem, 272, 490-496.  
9108163 S.R.Paalman, D.M.Noll, and N.D.Clarke (1997).
Formation of a covalent complex between methylguanine methyltransferase and DNA via disulfide bond formation between the active site cysteine and a thiol-containing analog of guanine.
  Nucleic Acids Res, 25, 1795-1801.  
9153417 T.K.Hazra, R.Roy, T.Biswas, D.T.Grabowski, A.E.Pegg, and S.Mitra (1997).
Specific recognition of O6-methylguanine in DNA by active site mutants of human O6-methylguanine-DNA methyltransferase.
  Biochemistry, 36, 5769-5776.  
8987998 A.A.Purmal, S.S.Wallace, and Y.W.Kow (1996).
The phosphodiester bond 3' to a deoxyuridine residue is crucial for substrate binding for uracil DNA N-glycosylase.
  Biochemistry, 35, 16630-16637.  
8676855 A.Taketomi, Y.Nakabeppu, K.Ihara, D.J.Hart, M.Furuichi, and M.Sekiguchi (1996).
Requirement for two conserved cysteine residues in the Ada protein of Escherichia coli for transactivation of the ada promoter.
  Mol Gen Genet, 250, 523-532.  
8942637 B.W.Allan, and N.O.Reich (1996).
Targeted base stacking disruption by the EcoRI DNA methyltransferase.
  Biochemistry, 35, 14757-14762.  
8650230 F.C.Christians, and L.A.Loeb (1996).
Novel human DNA alkyltransferases obtained by random substitution and genetic selection in bacteria.
  Proc Natl Acad Sci U S A, 93, 6124-6128.  
8913681 J.P.Turkenburg, and E.J.Dodson (1996).
Modern developments in molecular replacement.
  Curr Opin Struct Biol, 6, 604-610.  
8943065 J.S.Reese, O.N.Koç, K.M.Lee, L.Liu, J.A.Allay, W.P.Phillips, and S.L.Gerson (1996).
Retroviral transduction of a mutant methylguanine DNA methyltransferase gene into human CD34 cells confers resistance to O6-benzylguanine plus 1,3-bis(2-chloroethyl)-1-nitrosourea.
  Proc Natl Acad Sci U S A, 93, 14088-14093.  
8668540 K.Bender, M.Federwisch, U.Loggen, P.Nehls, and M.F.Rajewsky (1996).
Binding and repair of O6-ethylguanine in double-stranded oligodeoxynucleotides by recombinant human O6-alkylguanine-DNA alkyltransferase do not exhibit significant dependence on sequence context.
  Nucleic Acids Res, 24, 2087-2094.  
8952480 M.G.Fried, S.Kanugula, J.L.Bromberg, and A.E.Pegg (1996).
DNA binding mechanism of O6-alkylguanine-DNA alkyltransferase: stoichiometry and effects of DNA base composition and secondary structure on complex stability.
  Biochemistry, 35, 15295-15301.  
  8771196 Y.Zhang, C.S.Bond, S.Bailey, M.L.Cunningham, A.H.Fairlamb, and W.N.Hunter (1996).
The crystal structure of trypanothione reductase from the human pathogen Trypanosoma cruzi at 2.3 A resolution.
  Protein Sci, 5, 52-61.
PDB code: 1aog
7583113 B.Demple (1995).
Enzyme structures. DNA repair flips out.
  Curr Biol, 5, 719-721.  
  7868601 B.M.Saget, D.E.Shevell, and G.C.Walker (1995).
Alteration of lysine 178 in the hinge region of the Escherichia coli ada protein interferes with activation of ada, but not alkA, transcription.
  J Bacteriol, 177, 1268-1274.  
7697717 C.D.Mol, A.S.Arvai, G.Slupphaug, B.Kavli, I.Alseth, H.E.Krokan, and J.A.Tainer (1995).
Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis.
  Cell, 80, 869-878.  
7528896 E.Sledziewska-Gójska (1995).
Inactivation of O6-methylguanine-DNA methyltransferase in vivo by SN2 alkylating agents.
  Mutat Res, 336, 61-67.  
7773744 J.A.Tainer, M.M.Thayer, and R.P.Cunningham (1995).
DNA repair proteins.
  Curr Opin Struct Biol, 5, 20-26.  
8533156 L.H.Pearl, and R.Savva (1995).
DNA repair in three dimensions.
  Trends Biochem Sci, 20, 421-426.  
7606789 R.J.Roberts (1995).
On base flipping.
  Cell, 82, 9.  
7773746 X.Cheng (1995).
DNA modification by methyltransferases.
  Curr Opin Struct Biol, 5, 4.  
  8062817 A.Vrielink, W.Rüger, H.P.Driessen, and P.S.Freemont (1994).
Crystal structure of the DNA modifying enzyme beta-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose.
  EMBO J, 13, 3413-3422.
PDB codes: 1bgt 1bgu 2bgt 2bgu
7937881 B.M.Saget, and G.C.Walker (1994).
The Ada protein acts as both a positive and a negative modulator of Escherichia coli's response to methylating agents.
  Proc Natl Acad Sci U S A, 91, 9730-9734.  
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.  
  8050995 M.H.Lee, T.Ohta, and G.C.Walker (1994).
A monocysteine approach for probing the structure and interactions of the UmuD protein.
  J Bacteriol, 176, 4825-4837.  
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.