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PDBsum entry 1t39

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protein dna_rna links
Transferase/DNA PDB id
1t39
Jmol
Contents
Protein chains
151 a.a. *
DNA/RNA
* Residue conservation analysis
PDB id:
1t39
Name: Transferase/DNA
Title: Human o6-alkylguanine-DNA alkyltransferase covalently crosslinked to DNA
Structure: 5'-d( Gp Cp Cp Ap Tp Gp (E1x)p Cp Tp Ap Gp Tp A)- 3'. Chain: c, e. Engineered: yes. 5'-d( Tp Ap Cp Tp Ap Gp Cp Cp Ap Tp Gp Gp C)-3'. Chain: d, f. Engineered: yes. Methylated-DNA--protein-cysteine methyltransferase.
Source: Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Gene: mgmt. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Trimer (from PQS)
Resolution:
3.30Å     R-factor:   0.296     R-free:   0.344
Authors: D.S.Daniels,T.T.Woo,K.X.Luu,D.M.Noll,N.D.Clarke,A.E.Pegg, J.A.Tainer
Key ref:
D.S.Daniels et al. (2004). DNA binding and nucleotide flipping by the human DNA repair protein AGT. Nat Struct Mol Biol, 11, 714-720. PubMed id: 15221026 DOI: 10.1038/nsmb791
Date:
25-Apr-04     Release date:   13-Jul-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P16455  (MGMT_HUMAN) -  Methylated-DNA--protein-cysteine methyltransferase
Seq:
Struc:
207 a.a.
151 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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
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    
 
 
DOI no: 10.1038/nsmb791 Nat Struct Mol Biol 11:714-720 (2004)
PubMed id: 15221026  
 
 
DNA binding and nucleotide flipping by the human DNA repair protein AGT.
D.S.Daniels, T.T.Woo, K.X.Luu, D.M.Noll, N.D.Clarke, A.E.Pegg, J.A.Tainer.
 
  ABSTRACT  
 
O(6)-alkylguanine-DNA alkyltransferase (AGT), or O(6)-methylguanine-DNA methyltransferase (MGMT), prevents mutations and apoptosis resulting from alkylation damage to guanines. AGT irreversibly transfers the alkyl lesion to an active site cysteine in a stoichiometric, direct damage reversal pathway. AGT expression therefore elicits tumor resistance to alkylating chemotherapies, and AGT inhibitors are in clinical trials. We report here structures of human AGT in complex with double-stranded DNA containing the biological substrate O(6)-methylguanine or crosslinked to the mechanistic inhibitor N(1),O(6)-ethanoxanthosine. The prototypical DNA major groove-binding helix-turn-helix (HTH) motif mediates unprecedented minor groove DNA binding. This binding architecture has advantages for DNA repair and nucleotide flipping, and provides a paradigm for HTH interactions in sequence-independent DNA-binding proteins like RecQ and BRCA2. Structural and biochemical results further support an unpredicted role for Tyr114 in nucleotide flipping through phosphate rotation and an efficient kinetic mechanism for locating alkylated bases.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Minor groove binding, nucleotide flipping and O6-akylguanine recognition by AGT. (a,b) The recognition helix binds deeply within the minor groove, placing Arg128 in the base stack to replace the extrahelical O6-methylguanine. The HTH motif and Arg128 side chain are green, DNA nucleotides are orange and the DNA phosphate backbone is yellow. (c) Cutaway view of the C145S -O6-methylguanine active site. (d) AGT -N1,O6-ethanoxanthine active site. In c and d, Tyr114 induces rotation of the 3' phosphate of the nucleotide to promote flipping of the target nucleotide. Hydrogen bonds from Ser159, Cys145, Val145 and Tyr114 mediate binding of O6-methylguanine, Ser159 and Tyr114 of N1, O6-ethanoxanthine.
Figure 6.
Figure 6. The minor groove DNA-binding mechanism of AGT expands the HTH repertoire. (a) The catabolite activator protein (CAP) exhibits classic major groove binding by the recognition helix. (b) hRFX1 revealed recognition of the major groove by an adjacent DNA-binding wing. (c) AGT is the first HTH protein known to bind the minor groove, and does so using the recognition helix. The recognition helices (RH) of each protein are identically aligned and only one monomer of CAP and hRFX1, which bind DNA as dimers, is shown.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 714-720) copyright 2004.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20876689 E.Fadda, and R.Pomès (2011).
On the molecular basis of uracil recognition in DNA: comparative study of T-A versus U-A structure, dynamics and open base pair kinetics.
  Nucleic Acids Res, 39, 767-780.  
21187151 L.M.Hellman, C.Zhao, M.Melikishvili, X.Tao, J.E.Hopper, S.W.Whiteheart, and M.G.Fried (2011).
Histidine-tag-directed chromophores for tracer analyses in the analytical ultracentrifuge.
  Methods, 54, 31-38.  
21059809 T.Onodera, K.Morino, S.Tokishita, R.Morita, R.Masui, S.Kuramitsu, and T.Ohta (2011).
Role of alkyltransferase-like (ATL) protein in repair of methylated DNA lesions in Thermus thermophilus.
  Mutagenesis, 26, 303-308.  
20714506 B.Chen, H.Liu, X.Sun, and C.G.Yang (2010).
Mechanistic insight into the recognition of single-stranded and double-stranded DNA substrates by ABH2 and ABH3.
  Mol Biosyst, 6, 2143-2149.  
20036207 C.Zhao, L.M.Hellman, X.Zhan, W.S.Bowman, S.W.Whiteheart, and M.G.Fried (2010).
Hexahistidine-tag-specific optical probes for analyses of proteins and their interactions.
  Anal Biochem, 399, 237-245.  
20714665 F.P.McManus, Q.Fang, J.D.Booth, A.M.Noronha, A.E.Pegg, and C.J.Wilds (2010).
Synthesis and characterization of an O(6)-2'-deoxyguanosine-alkyl-O(6)-2'-deoxyguanosine interstrand cross-link in a 5'-GNC motif and repair by human O(6)-alkylguanine-DNA alkyltransferase.
  Org Biomol Chem, 8, 4414-4426.  
20502938 J.L.Tubbs, and J.A.Tainer (2010).
Alkyltransferase-like proteins: molecular switches between DNA repair pathways.
  Cell Mol Life Sci, 67, 3749-3762.  
20159463 K.Kitano, S.Y.Kim, and T.Hakoshima (2010).
Structural basis for DNA strand separation by the unconventional winged-helix domain of RecQ helicase WRN.
  Structure, 18, 177-187.
PDB code: 3aaf
20178313 K.Lu, W.Ye, L.Zhou, L.B.Collins, X.Chen, A.Gold, L.M.Ball, and J.A.Swenberg (2010).
Structural characterization of formaldehyde-induced cross-links between amino acids and deoxynucleosides and their oligomers.
  J Am Chem Soc, 132, 3388-3399.  
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.  
20334529 R.Rohs, X.Jin, S.M.West, R.Joshi, B.Honig, and R.S.Mann (2010).
Origins of specificity in protein-DNA recognition.
  Annu Rev Biochem, 79, 233-269.  
20061189 Y.Wu, and R.M.Brosh (2010).
Distinct roles of RECQ1 in the maintenance of genomic stability.
  DNA Repair (Amst), 9, 315-324.  
19892775 Y.Zhong, Y.Huang, Y.Huang, T.Zhang, C.Ma, S.Zhang, W.Fan, H.Chen, J.Qian, and D.Lu (2010).
Effects of O6-methylguanine-DNA methyltransferase (MGMT) polymorphisms on cancer: a meta-analysis.
  Mutagenesis, 25, 83-95.  
19472322 A.G.Kalapila, N.A.Loktionova, and A.E.Pegg (2009).
Effect of O6-alkylguanine-DNA alkyltransferase on genotoxicity of epihalohydrins.
  Environ Mol Mutagen, 50, 502-514.  
19949442 A.Vindigni, and I.D.Hickson (2009).
RecQ helicases: multiple structures for multiple functions?
  HFSP J, 3, 153-164.  
19358853 C.A.Adams, M.Melikishvili, D.W.Rodgers, J.J.Rasimas, A.E.Pegg, and M.G.Fried (2009).
Topologies of complexes containing O6-alkylguanine-DNA alkyltransferase and DNA.
  J Mol Biol, 389, 248-263.  
19145606 C.G.Yang, K.Garcia, and C.He (2009).
Damage detection and base flipping in direct DNA alkylation repair.
  Chembiochem, 10, 417-423.  
19852088 C.Yi, C.G.Yang, and C.He (2009).
A non-heme iron-mediated chemical demethylation in DNA and RNA.
  Acc Chem Res, 42, 519-529.  
19465399 D.Kim, S.Reddy, D.Y.Kim, A.Rich, S.Lee, K.K.Kim, and Y.G.Kim (2009).
Base extrusion is found at helical junctions between right- and left-handed forms of DNA and RNA.
  Nucleic Acids Res, 37, 4353-4359.  
19516334 J.L.Tubbs, V.Latypov, S.Kanugula, A.Butt, M.Melikishvili, R.Kraehenbuehl, O.Fleck, A.Marriott, A.J.Watson, B.Verbeek, G.McGown, M.Thorncroft, M.F.Santibanez-Koref, C.Millington, A.S.Arvai, M.D.Kroeger, L.A.Peterson, D.M.Williams, M.G.Fried, G.P.Margison, A.E.Pegg, and J.A.Tainer (2009).
Flipping of alkylated DNA damage bridges base and nucleotide excision repair.
  Nature, 459, 808-813.
PDB codes: 3gva 3gx4 3gyh
19756275 P.K.Shukla, and P.C.Mishra (2009).
Repair of O6-methylguanine to guanine by cysteine in the absence and presence of histidine and by cysteine thiolate anion: a quantum chemical study.
  Phys Chem Chem Phys, 11, 8191-8202.  
19531487 R.Guza, L.Ma, Q.Fang, A.E.Pegg, and N.Tretyakova (2009).
Cytosine methylation effects on the repair of O6-methylguanines within CG dinucleotides.
  J Biol Chem, 284, 22601-22610.  
19480393 R.L.Loeber, E.D.Michaelson-Richie, S.G.Codreanu, D.C.Liebler, C.R.Campbell, and N.Y.Tretyakova (2009).
Proteomic analysis of DNA-protein cross-linking by antitumor nitrogen mustards.
  Chem Res Toxicol, 22, 1151-1162.  
19200715 S.Schneider, S.Schorr, and T.Carell (2009).
Crystal structure analysis of DNA lesion repair and tolerance mechanisms.
  Curr Opin Struct Biol, 19, 87-95.  
19421793 S.Tiwari, and P.C.Mishra (2009).
A quantum chemical study of repair of O6-methylguanine to guanine by tyrosine: evaluation of the winged helix-turn-helix model.
  J Mol Model, 15, 1407-1415.  
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.  
19635647 Y.Zhu, J.Hu, Y.Hu, and W.Liu (2009).
Targeting DNA repair pathways: a novel approach to reduce cancer therapeutic resistance.
  Cancer Treat Rev, 35, 590-596.  
18712882 A.G.Kalapila, N.A.Loktionova, and A.E.Pegg (2008).
Alkyltransferase-mediated toxicity of 1,3-butadiene diepoxide.
  Chem Res Toxicol, 21, 1851-1861.  
18291317 A.Gautier, A.Juillerat, C.Heinis, I.R.Corrêa, M.Kindermann, F.Beaufils, and K.Johnsson (2008).
An engineered protein tag for multiprotein labeling in living cells.
  Chem Biol, 15, 128-136.  
18319248 D.Hazelbaker, M.A.Azaro, and A.Landy (2008).
A biotin interference assay highlights two different asymmetric interaction profiles for lambda integrase arm-type binding sites in integrative versus excisive recombination.
  J Biol Chem, 283, 12402-12414.  
18408731 E.D.Garcin, D.J.Hosfield, S.A.Desai, B.J.Haas, M.Björas, R.P.Cunningham, and J.A.Tainer (2008).
DNA apurinic-apyrimidinic site binding and excision by endonuclease IV.
  Nat Struct Mol Biol, 15, 515-522.
PDB codes: 2nq9 2nqh 2nqj
18973327 G.T.Pauly, N.A.Loktionova, Q.Fang, S.L.Vankayala, W.C.Guida, and A.E.Pegg (2008).
Substitution of aminomethyl at the meta-position enhances the inactivation of O6-alkylguanine-DNA alkyltransferase by O6-benzylguanine.
  J Med Chem, 51, 7144-7153.  
18353991 J.Hu, A.Ma, and A.R.Dinner (2008).
A two-step nucleotide-flipping mechanism enables kinetic discrimination of DNA lesions by AGT.
  Proc Natl Acad Sci U S A, 105, 4615-4620.  
19061338 M.Melikishvili, J.J.Rasimas, A.E.Pegg, and M.G.Fried (2008).
Interactions of human O(6)-alkylguanine-DNA alkyltransferase (AGT) with short double-stranded DNAs.
  Biochemistry, 47, 13754-13763.  
19055796 P.Slama, I.Filippis, and M.Lappe (2008).
Detection of protein catalytic residues at high precision using local network properties.
  BMC Bioinformatics, 9, 517.  
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.  
17996846 Q.Fang, N.A.Loktionova, R.C.Moschel, S.Javanmard, G.T.Pauly, and A.E.Pegg (2008).
Differential inactivation of polymorphic variants of human O6-alkylguanine-DNA alkyltransferase.
  Biochem Pharmacol, 75, 618-626.  
18669665 R.H.Porecha, and J.T.Stivers (2008).
Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils.
  Proc Natl Acad Sci U S A, 105, 10791-10796.  
18324787 R.Loeber, E.Michaelson, Q.Fang, C.Campbell, A.E.Pegg, and N.Tretyakova (2008).
Cross-linking of the DNA repair protein Omicron6-alkylguanine DNA alkyltransferase to DNA in the presence of antitumor nitrogen mustards.
  Chem Res Toxicol, 21, 787-795.  
17827238 T.Zhao, and A.R.Dinner (2008).
Apparent directional scanning for DNA repair.
  Biophys J, 94, 47-52.  
17482892 A.E.Pegg, Q.Fang, and N.A.Loktionova (2007).
Human variants of O6-alkylguanine-DNA alkyltransferase.
  DNA Repair (Amst), 6, 1071-1078.  
17700363 C.E.Hill, J.K.Wickliffe, A.T.Guerin, C.J.Kinslow, K.J.Wolfe, M.M.Ammenheuser, and S.Z.Abdel-Rahman (2007).
The L84F polymorphism in the O6-Methylguanine-DNA-Methyltransferase (MGMT) gene is associated with increased hypoxanthine phosphoribosyltransferase (HPRT) mutant frequency in lymphocytes of tobacco smokers.
  Pharmacogenet Genomics, 17, 743-753.  
17375187 I.Laponogov, D.A.Veselkov, M.K.Sohi, X.S.Pan, A.Achari, C.Yang, J.D.Ferrara, L.M.Fisher, and M.R.Sanderson (2007).
Breakage-reunion domain of Streptococcus pneumoniae topoisomerase IV: crystal structure of a gram-positive quinolone target.
  PLoS ONE, 2, e301.
PDB code: 2nov
17138560 J.J.Rasimas, S.R.Kar, A.E.Pegg, and M.G.Fried (2007).
Interactions of human O6-alkylguanine-DNA alkyltransferase (AGT) with short single-stranded DNAs.
  J Biol Chem, 282, 3357-3366.  
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.  
17105728 R.L.Eoff, A.Irimia, M.Egli, and F.P.Guengerich (2007).
Sulfolobus solfataricus DNA polymerase Dpo4 is partially inhibited by "wobble" pairing between O6-methylguanine and cytosine, but accurate bypass is preferred.
  J Biol Chem, 282, 1456-1467.
PDB codes: 2j6s 2j6t 2j6u
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.  
17005466 I.Sánchez-Pérez (2006).
DNA repair inhibitors in cancer treatment.
  Clin Transl Oncol, 8, 642-646.  
16697054 J.Ding, Z.H.Miao, L.H.Meng, and M.Y.Geng (2006).
Emerging cancer therapeutic opportunities target DNA-repair systems.
  Trends Pharmacol Sci, 27, 338-344.  
16935877 M.P.Killoran, and J.L.Keck (2006).
Sit down, relax and unwind: structural insights into RecQ helicase mechanisms.
  Nucleic Acids Res, 34, 4098-4105.  
16858410 O.Sundheim, C.B.Vågbø, M.Bjørås, M.M.Sousa, V.Talstad, P.A.Aas, F.Drabløs, H.E.Krokan, J.A.Tainer, and G.Slupphaug (2006).
Human ABH3 structure and key residues for oxidative demethylation to reverse DNA/RNA damage.
  EMBO J, 25, 3389-3397.
PDB code: 2iuw
16380375 S.Choudhary, K.M.Doherty, C.J.Handy, J.M.Sayer, H.Yagi, D.M.Jerina, and R.M.Brosh (2006).
Inhibition of Werner syndrome helicase activity by benzo[a]pyrene diol epoxide adducts can be overcome by replication protein A.
  J Biol Chem, 281, 6000-6009.  
15934048 A.Juillerat, C.Heinis, I.Sielaff, J.Barnikow, H.Jaccard, B.Kunz, A.Terskikh, and K.Johnsson (2005).
Engineering substrate specificity of O6-alkylguanine-DNA alkyltransferase for specific protein labeling in living cells.
  Chembiochem, 6, 1263-1269.  
16340006 R.K.Neely, D.Daujotyte, S.Grazulis, S.W.Magennis, D.T.Dryden, S.Klimasauskas, and A.C.Jones (2005).
Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI-DNA complexes.
  Nucleic Acids Res, 33, 6953-6960.
PDB codes: 2c7o 2c7p 2c7q 2c7r
16027108 S.J.Pearson, J.Ferguson, M.Santibanez-Koref, and G.P.Margison (2005).
Inhibition of O6-methylguanine-DNA methyltransferase by an alkyltransferase-like protein from Escherichia coli.
  Nucleic Acids Res, 33, 3837-3844.  
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.  
16229032 T.Peng, and K.Nakatani (2005).
Binding of naphthyridine carbamate dimer to the (CGG)n repeat results in the disruption of the G-C base pairing.
  Angew Chem Int Ed Engl, 44, 7280-7283.  
15280878 T.J.Begley, and L.D.Samson (2004).
Reversing DNA damage with a directional bias.
  Nat Struct Mol Biol, 11, 688-690.  
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.