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 

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:  

  • 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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Exodeoxyribonuclease
A, B
265Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)Mutation(s): 1 
Find proteins for O26314 (Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H))
Go to UniProtKB:  O26314
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*GP*TP*AP*CP*TP*AP*CP*G)-3'H9N/A
Entity ID: 3
MoleculeChainsLengthOrganism
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
PO4
Query on PO4

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

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

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UPS
Query on UPS
I
DNA linkingC9 H13 N2 O7 P SDU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 100.354α = 90.00
b = 79.337β = 90.00
c = 98.550γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
MAR345data collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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