PDBsum entry 1mgt

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protein ligands links
Transferase PDB id
Protein chain
169 a.a. *
SO4 ×3
Waters ×129
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of o6-methylguanine-DNA methyltransferase hyperthermophilic archaeon pyrococcus kodakaraensis strain
Structure: Protein (o6-methylguanine-DNA methyltransferase). Chain: a. Synonym: mgmt. Engineered: yes
Source: Thermococcus kodakarensis. Organism_taxid: 69014. Strain: kod1. Expressed in: escherichia coli. Expression_system_taxid: 562
1.80Å     R-factor:   0.173     R-free:   0.218
Authors: H.Hashimoto,T.Inoue,M.Nishioka,S.Fujiwara,M.Takagi,T.Imanaka
Key ref:
H.Hashimoto et al. (1999). Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase. J Mol Biol, 292, 707-716. PubMed id: 10497033 DOI: 10.1006/jmbi.1999.3100
12-Jan-99     Release date:   07-Jan-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
O74023  (OGT_PYRKO) -  Methylated-DNA--protein-cysteine methyltransferase
174 a.a.
169 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: 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
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     response to DNA damage stimulus   4 terms 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1006/jmbi.1999.3100 J Mol Biol 292:707-716 (1999)
PubMed id: 10497033  
Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase.
H.Hashimoto, T.Inoue, M.Nishioka, S.Fujiwara, M.Takagi, T.Imanaka, Y.Kai.
The crystal structure of O6-methylguanine-DNA methyltransferase (EC of hyperthermophilic archaeon Pyrococcuskodakaraensis strain KOD1 (Pk -MGMT) was determined by single isomorphous replacement method with anomalous scattering (SIRAS) at 1.8 A resolution. The archaeal protein is extremely thermostable and repairs alkylated DNA by suicidal alkyl transfer from guanine O6 to its own cysteine residue. Archaea constitute the third primary kingdom of living organisms, sharing characteristics with procaryotic and eucaryotic cells. They live in various extreme environments and are thought to include the most ancient organisms on the earth. Structural studies on hyperthermophilic archaeal proteins reveal the structural features essential for stability under the extreme environments in which these organisms live, and will provide the structural basis required for stabilizing various mesophilic proteins for industrial applications. Here, we report the crystal structure of Pk-MGMT and structural comparison of Pk-MGMT and methyltransferase homologue from Escherichia coli (AdaC, C-terminal fragment of Ada protein). Analyses of solvent-accessible surface area (SASA) reveals a large discrepancy between Pk-MGMT and AdaC with respect to the property of the ASA. In the Pk-MGMT structure, the intra-helix ion-pairs contribute to reinforce stability of alpha-helices. The inter-helix ion-pairs exist in the interior of Pk-MGMT and stabilize internal packing of tertiary structure. Furthermore, structural features of helix cappings, intra and inter-helix ion-pairs are found around the active-site structure in Pk-MGMT.
  Selected figure(s)  
Figure 1.
Figure 1. (a) Schematic drawing of the crystal structure of Pk-MGMT. Aromatic clusters are displayed by ball-and-stick models. The wing loop from the end of fi6 to the start of g-helix is colored yellow, as shown in Figure 4(b). (b) Schematic drawing of the crystal structure of AdaC. The three inserted residues, K126, Al27 and Vl28, are shown by ball-and-stick models.
Figure 4.
Figure 4. (a) The DNA-binding region of PK-MGMT, as viewed from the bottom of Figure l(a). DNA binds from the left-hand side. The N-cap residues and Nl proline residues are colored green. Intra-helix ion-pairs in the c and d-helices are shown as ball-and-stick models. Red and blue colored cages are the IF,/ - IF,1 map and the IF,/ - IF,1 omit map contoured at 2.00, respectively. The IF,1 - IF,1 omit map was calculated to omit E98 in the final models. The maps suggest dual conformation of E98. (b) The active-site environment of Pk-MGMT, as viewed from the top of Figure l(a). DNA binds from the bottom side. Extra ion-pairs are shown as ball-andstick models (colored dark gray). The semitransparent helix is the a-helix in the N-terminal domain. The helix hangs on to the active site by two inter-helix ion-pairs (R39-El59 and R50-E93). The wing loop is colored yellow. Stability of helical conformation in g-helix is reinforced by the E158-K161 intra-helix ion-pair.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1999, 292, 707-716) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19558674 Y.Zivanovic, J.Armengaud, A.Lagorce, C.Leplat, P.Guérin, M.Dutertre, V.Anthouard, P.Forterre, P.Wincker, and F.Confalonieri (2009).
Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea.
  Genome Biol, 10, R70.  
18780158 A.K.Williamson (2008).
Structural and functional aspects of the MSP (PsbO) and study of its differences in thermophilic versus mesophilic organisms.
  Photosynth Res, 98, 365-389.  
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.  
18422647 Y.Koga, R.Katsumi, D.J.You, H.Matsumura, K.Takano, and S.Kanaya (2008).
Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form.
  FEBS J, 275, 2632-2643.
PDB code: 2zf5
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
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
16464003 Y.Mishina, E.M.Duguid, and C.He (2006).
Direct reversal of DNA alkylation damage.
  Chem Rev, 106, 215-232.  
15508124 M.Sugahara, Y.Nodake, M.Sugahara, and N.Kunishima (2005).
Crystal structure of dehydroquinate synthase from Thermus thermophilus HB8 showing functional importance of the dimeric state.
  Proteins, 58, 249-252.
PDB code: 1ujn
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.  
15326599 B.N.Dominy, H.Minoux, and C.L.Brooks (2004).
An electrostatic basis for the stability of thermophilic proteins.
  Proteins, 57, 128-141.  
15040447 B.Sedgwick (2004).
Repairing DNA-methylation damage.
  Nat Rev Mol Cell Biol, 5, 148-157.  
15356290 H.P.Shanahan, M.A.Garcia, S.Jones, and J.M.Thornton (2004).
Identifying DNA-binding proteins using structural motifs and the electrostatic potential.
  Nucleic Acids Res, 32, 4732-4741.  
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.  
  16233593 K.Shiraki, S.Nishikori, S.Fujiwara, T.Imanaka, and M.Takagi (2004).
Contribution of protein-surface ion pairs of a hyperthermophilic protein on thermal and thermodynamic stability.
  J Biosci Bioeng, 97, 75-77.  
12529358 H.Sakuraba, H.Tsuge, I.Shimoya, R.Kawakami, S.Goda, Y.Kawarabayasi, N.Katunuma, H.Ago, M.Miyano, and T.Ohshima (2003).
The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix.
  J Biol Chem, 278, 10799-10806.
PDB code: 1n7k
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.  
12771208 S.Jones, J.A.Barker, I.Nobeli, and J.M.Thornton (2003).
Using structural motif templates to identify proteins with DNA binding function.
  Nucleic Acids Res, 31, 2811-2823.  
12837801 X.Wang, X.He, S.Yang, X.An, W.Chang, and D.Liang (2003).
Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.
  J Bacteriol, 185, 4248-4255.
PDB code: 1np2
12070156 N.Maeda, T.Kanai, H.Atomi, and T.Imanaka (2002).
The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability.
  J Biol Chem, 277, 31656-31662.  
  16233344 S.Fujiwara (2002).
Extremophiles: developments of their special functions and potential resources.
  J Biosci Bioeng, 94, 518-525.  
12112867 T.Imanaka, and H.Atomi (2002).
Catalyzing "hot" reactions: enzymes from hyperthermophilic Archaea.
  Chem Rec, 2, 149-163.  
11238984 C.Vieille, and G.J.Zeikus (2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
  Microbiol Mol Biol Rev, 65, 1.  
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.  
11166997 Y.Hakamada, Y.Hatada, T.Ozawa, K.Ozaki, T.Kobayashi, and S.Ito (2001).
Identification of thermostabilizing residues in a Bacillus alkaline cellulase by construction of chimeras from mesophilic and thermostable enzymes and site-directed mutagenesis.
  FEMS Microbiol Lett, 195, 67-72.  
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
11053387 M.Nakatani, S.Ezaki, H.Atomi, and T.Imanaka (2000).
A DNA ligase from a hyperthermophilic archaeon with unique cofactor specificity.
  J Bacteriol, 182, 6424-6433.  
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.