6JUN

MsDpo4-DNA complex 3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation 3D Report Full Report



Literature

A polar filter in DNA polymerases prevents ribonucleotide incorporation.

Johnson, M.K.Kottur, J.Nair, D.T.

(2019) Nucleic Acids Res 47: 10693-10705

  • DOI: 10.1093/nar/gkz792
  • Primary Citation of Related Structures:  
    6JUR, 6JUQ, 6JUS, 6JUL, 6JUN, 6JUM, 6JUP, 6JUO

  • PubMed Abstract: 
  • The presence of ribonucleotides in DNA can lead to genomic instability and cellular lethality. To prevent adventitious rNTP incorporation, the majority of the DNA polymerases (dPols) possess a steric filter. The dPol named MsDpo4 (Mycobacterium smegm ...

    The presence of ribonucleotides in DNA can lead to genomic instability and cellular lethality. To prevent adventitious rNTP incorporation, the majority of the DNA polymerases (dPols) possess a steric filter. The dPol named MsDpo4 (Mycobacterium smegmatis) naturally lacks this steric filter and hence is capable of rNTP addition. The introduction of the steric filter in MsDpo4 did not result in complete abrogation of the ability of this enzyme to incorporate ribonucleotides. In comparison, DNA polymerase IV (PolIV) from Escherichia coli exhibited stringent selection for deoxyribonucleotides. A comparison of MsDpo4 and PolIV led to the discovery of an additional polar filter responsible for sugar selectivity. Thr43 represents the filter in PolIV and this residue forms interactions with the incoming nucleotide to draw it closer to the enzyme surface. As a result, the 2'-OH in rNTPs will clash with the enzyme surface, and therefore ribonucleotides cannot be accommodated in the active site in a conformation compatible with productive catalysis. The substitution of the equivalent residue in MsDpo4-Cys47, with Thr led to a drastic reduction in the ability of the mycobacterial enzyme to incorporate rNTPs. Overall, our studies evince that the polar filter serves to prevent ribonucleotide incorporation by dPols.


    Organizational Affiliation

    Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, Faridabad 121001, India.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase IVA, F356Mycolicibacterium smegmatis MC2 155Mutation(s): 2 
Gene Names: MSMEG_1014MSMEG_2294dinB
EC: 2.7.7.7
Find proteins for A0QR77 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0QR77 
Go to UniProtKB:  A0QR77
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(P*TP*AP*GP*GP*AP*CP*CP*C)-3')B, C, G, H18Mycolicibacterium smegmatis
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    0KX
    Query on 0KX

    Download CCD File 
    A, F
    2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine
    C9 H17 N4 O12 P3
    STYMTWKSQLVXJN-SHYZEUOFSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 2.51 Å
    • R-Value Free: 0.257 
    • R-Value Work: 0.221 
    • R-Value Observed: 0.223 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 53.92α = 90
    b = 81.32β = 90
    c = 210.21γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    MOSFLMdata reduction
    SCALAdata scaling
    Cootmodel building
    PHENIXrefinement
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Department of Biotechnology (India)IndiaIntramural

    Revision History 

    • Version 1.0: 2020-02-19
      Type: Initial release