1MGT

CRYSTAL STRUCTURE OF O6-METHYLGUANINE-DNA METHYLTRANSFERASE FROM HYPERTHERMOPHILIC ARCHAEON PYROCOCCUS KODAKARAENSIS STRAIN KOD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Hyperthermostable protein structure maintained by intra and inter-helix ion-pairs in archaeal O6-methylguanine-DNA methyltransferase.

Hashimoto, H.Inoue, T.Nishioka, M.Fujiwara, S.Takagi, M.Imanaka, T.Kai, Y.

(1999) J Mol Biol 292: 707-716

  • DOI: 10.1006/jmbi.1999.3100
  • Primary Citation of Related Structures:  
    1MGT

  • PubMed Abstract: 
  • The crystal structure of O6-methylguanine-DNA methyltransferase (EC 2.1.1.63) of hyperthermophilic archaeon Pyrococcuskodakaraensis strain KOD1 (Pk -MGMT) was determined by single isomorphous replacement method with anomalous scattering (SIRAS) at 1. ...

    The crystal structure of O6-methylguanine-DNA methyltransferase (EC 2.1.1.63) 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.


    Related Citations: 
    • Crystallization and Preliminary X-Ray Crystallographic Analysis of Archaeal O6-Methylguanine-DNA Methyltransferase
      Hashimoto, H., Nishioka, M., Inoue, T., Fujiwara, S., Takagi, M., Imanaka, T., Kai, Y.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 1395

    Organizational Affiliation

    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, 565-0871, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN (O6-METHYLGUANINE-DNA METHYLTRANSFERASE)A174Thermococcus kodakarensis KOD1Mutation(s): 0 
Gene Names: ogtmgtkTK1971
EC: 2.1.1.63
Find proteins for O74023 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1))
Explore O74023 
Go to UniProtKB:  O74023
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.23α = 90
b = 86.22β = 90
c = 39.83γ = 90
Software Package:
Software NamePurpose
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-07
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance