3G2C

Mth0212 in complex with a short ssDNA (CGTA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.204 
  • R-Value Observed: 0.207 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal Structure Analysis of DNA Uridine Endonuclease Mth212 Bound to DNA

Lakomek, K.Dickmanns, A.Ciirdaeva, E.Schomacher, L.Ficner, R.

(2010) J Mol Biol 399: 604-617

  • DOI: 10.1016/j.jmb.2010.04.044
  • Primary Citation of Related Structures:  
    3G4T, 3G8V, 3G91, 3FZI, 3GA6, 3G1K, 3G38, 3G2C, 3G2D, 3G3Y

  • PubMed Abstract: 
  • The reliable repair of pre-mutagenic U/G mismatches that originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms, any uracil base in DNA is attacked by uracil DNA glycosylas ...

    The reliable repair of pre-mutagenic U/G mismatches that originated from hydrolytic cytosine deamination is crucial for the maintenance of the correct genomic information. In most organisms, any uracil base in DNA is attacked by uracil DNA glycosylases (UDGs), but at least in Methanothermobacter thermautotrophicus DeltaH, an alternative strategy has evolved. The exonuclease III homologue Mth212 from the thermophilic archaeon M. thermautotrophicus DeltaH exhibits a DNA uridine endonuclease activity in addition to the apyrimidinic/apurinic site endonuclease and 3'-->5'exonuclease functions. Mth212 alone compensates for the lack of a UDG in a single-step reaction thus substituting the two-step pathway that requires the consecutive action of UDG and apyrimidinic/apurinic site endonuclease. In order to gain deeper insight into the structural basis required for the specific uridine recognition by Mth212, we have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 A, suggesting key residues for the uridine endonuclease activity. The insertion of the side chain of Arg209 into the DNA helical base stack resembles interactions observed in human UDG and seems to be crucial for the uridine recognition. In addition, Ser171, Asn153, and Lys125 in the substrate binding pocket appear to have important functions in the discrimination of aberrant uridine against naturally occurring thymidine and cytosine residues in double-stranded DNA.


    Related Citations: 
    • The Methanothermobacter thermautotrophicus ExoIII homologue Mth212 is a DNA uridine endonuclease
      Georg, J., Schomacher, L., Chong, J.P.J., Majernik, A.I., Raabe, M., Urlaub, H., Muller, S., Ciirdaeva, E., Kramer, W., Fritz, H.-J.
      (2006) Nucleic Acids Res 34: 5325

    Organizational Affiliation

    Department of Molecular Structural Biology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Justus-von-Liebig Weg 11, D-37077 Göttingen, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ExodeoxyribonucleaseAB265Methanothermobacter thermautotrophicus str. Delta HMutation(s): 1 
Gene Names: mth0212MTH212MTH_212
EC: 3.1.11.2 (PDB Primary Data), 4.2.99.18 (UniProt)
Find proteins for O26314 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Explore O26314 
Go to UniProtKB:  O26314
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(P*CP*GP*TP*A)-3'I4N/A
    Small Molecules
    Ligands 3 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PO4
    Query on PO4

    Download CCD File 
    A, B
    PHOSPHATE ION
    O4 P
    NBIIXXVUZAFLBC-UHFFFAOYSA-K
     Ligand Interaction
    GOL
    Query on GOL

    Download CCD File 
    A, I
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download CCD File 
    A, B
    MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.30 Å
    • R-Value Free: 0.263 
    • R-Value Work: 0.204 
    • R-Value Observed: 0.207 
    • Space Group: P 32
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 80.325α = 90
    b = 80.325β = 90
    c = 79.611γ = 120
    Software Package:
    Software NamePurpose
    DENZOdata reduction
    SCALEPACKdata scaling
    MOLREPphasing
    REFMACrefinement
    PDB_EXTRACTdata extraction
    MAR345data collection
    HKL-2000data reduction
    HKL-2000data scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2010-03-09
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Version format compliance
    • Version 1.2: 2014-02-12
      Changes: Derived calculations
    • Version 1.3: 2017-11-01
      Changes: Refinement description