6TC9

Crystal structure of MutM from Neisseria meningitidis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.238 
  • R-Value Observed: 0.240 

wwPDB Validation 3D Report Full Report



Literature

Conformational changes of DNA repair glycosylase MutM triggered by DNA binding.

Landova, B.Silhan, J.

(2020) FEBS Lett 

  • DOI: 10.1002/1873-3468.13876
  • Primary Citation of Related Structures:  
    6TC6, 6TC9

  • PubMed Abstract: 
  • Bacterial MutM is a DNA repair glycosylase removing DNA damage generated from oxidative stress and, therefore, preventing mutations and genomic instability. MutM belongs to the Fpg/Nei family of prokaryotic enzymes sharing structural and functional s ...

    Bacterial MutM is a DNA repair glycosylase removing DNA damage generated from oxidative stress and, therefore, preventing mutations and genomic instability. MutM belongs to the Fpg/Nei family of prokaryotic enzymes sharing structural and functional similarities with their eukaryotic counterparts, for example, NEIL1-NEIL3. Here, we present two crystal structures of MutM from pathogenic Neisseria meningitidis: a MutM holoenzyme and MutM bound to DNA. The free enzyme exists in an open conformation, while upon binding to DNA, both the enzyme and DNA undergo substantial structural changes and domain rearrangement. Our data show that not only NEI glycosylases but also the MutMs undergo dramatic conformational changes. Moreover, crystallographic data support the previously published observations that MutM enzymes are rather flexible and dynamic molecules.


    Organizational Affiliation

    Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague, Czech Republic.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Formamidopyrimidine-DNA glycosylaseAC275Neisseria meningitidis alpha522Mutation(s): 0 
Gene Names: mutMfpgNMALPHA522_0971
EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
Find proteins for I4E596 (Neisseria meningitidis alpha522)
Explore I4E596 
Go to UniProtKB:  I4E596
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA containing abasic site analogueD, G14synthetic construct
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNAB, F14synthetic construct
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      ZN
      Query on ZN

      Download CCD File 
      A, C
      ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      MG
      Query on MG

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

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 2.17 Å
      • R-Value Free: 0.281 
      • R-Value Work: 0.238 
      • R-Value Observed: 0.240 
      • Space Group: C 1 2 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 130.77α = 90
      b = 80.38β = 89.95
      c = 83.62γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement
      XSCALEdata processing
      PHASERphasing
      XDSdata scaling
      XDSdata reduction

      Structure Validation

      View Full Validation Report



      Entry History & Funding Information

      Deposition Data


      Funding OrganizationLocationGrant Number
      Czech Academy of SciencesCzech Republic17-21649Y

      Revision History 

      • Version 1.0: 2020-09-16
        Type: Initial release