3G3C

Mth0212 (WT) in complex with a 6bp dsDNA containing a single one nucleotide long 3'-overhang


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.236 
  • R-Value Observed: 0.239 

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(*CP*GP*TP*AP*CP*TP*AP*CP*G)-3'H9N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*GP*TP*AP*(UPS)P*TP*AP*CP*G)-3'I9N/A
      Small Molecules
      Ligands 3 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      MRD
      Query on MRD

      Download CCD File 
      A
      (4R)-2-METHYLPENTANE-2,4-DIOL
      C6 H14 O2
      SVTBMSDMJJWYQN-RXMQYKEDSA-N
       Ligand Interaction
      PO4
      Query on PO4

      Download CCD File 
      A, B
      PHOSPHATE ION
      O4 P
      NBIIXXVUZAFLBC-UHFFFAOYSA-K
       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: 3.04 Å
      • R-Value Free: 0.294 
      • R-Value Work: 0.236 
      • R-Value Observed: 0.239 
      • Space Group: P 21 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 100.354α = 90
      b = 79.337β = 90
      c = 98.55γ = 90
      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