6KIJ

Crystal structure of yedK with ssDNA containing an abasic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Molecular basis of abasic site sensing in single-stranded DNA by the SRAP domain of E. coli yedK.

Wang, N.Bao, H.Chen, L.Liu, Y.Li, Y.Wu, B.Huang, H.

(2019) Nucleic Acids Res 47: 10388-10399

  • DOI: 10.1093/nar/gkz744
  • Primary Citation of Related Structures:  
    6KBU, 6KBX, 6KBZ, 6KBS, 6KCQ, 6KIJ

  • PubMed Abstract: 
  • HMCES and yedK were recently identified as sensors of abasic sites in ssDNA. In this study, we present multiple crystal structures captured in the apo-, nonspecific-substrate-binding, specific-substrate-binding, and product-binding states of yedK. In com ...

    HMCES and yedK were recently identified as sensors of abasic sites in ssDNA. In this study, we present multiple crystal structures captured in the apo-, nonspecific-substrate-binding, specific-substrate-binding, and product-binding states of yedK. In combination with biochemical data, we unveil the molecular basis of AP site sensing in ssDNA by yedK. Our results indicate that yedK has a strong preference for AP site-containing ssDNA over native ssDNA and that the conserved Glu105 residue is important for identifying AP sites in ssDNA. Moreover, our results reveal that a thiazolidine linkage is formed between yedK and AP sites in ssDNA, with the residues that stabilize the thiazolidine linkage important for the formation of DNA-protein crosslinks between yedK and the AP sites. We propose that our findings offer a unique platform to develop yedK and other SRAP domain-containing proteins as tools for detecting abasic sites in vitro and in vivo.


    Organizational Affiliation

    Department of Biology, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SOS response-associated protein B227Escherichia coliMutation(s): 0 
Gene Names: yedKC4J69_22885ECTO6_01993EFV06_12905EFV16_12155SAMEA3472108_01185SAMEA3752559_04370
EC: 3.4
Find proteins for P76318 (Escherichia coli (strain K12))
Explore P76318 
Go to UniProtKB:  P76318
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*AP*TP*TP*CP*GP*TP*CP*G)-3')A9Escherichia coli
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PED
    Query on PED

    Download Ideal Coordinates CCD File 
    B
    PENTANE-3,4-DIOL-5-PHOSPHATE
    C5 H13 O6 P
    FQKLTSRHTQGSQZ-CRCLSJGQSA-N
     Ligand Interaction
    GOL
    Query on GOL

    Download Ideal Coordinates CCD File 
    B
    GLYCEROL
    C3 H8 O3
    PEDCQBHIVMGVHV-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.58 Å
    • R-Value Free: 0.183 
    • R-Value Work: 0.152 
    • R-Value Observed: 0.154 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 47.444α = 90
    b = 44.08β = 102.33
    c = 55.148γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    SCALEPACKdata scaling
    PDB_EXTRACTdata extraction
    HKL-3000data reduction
    PHASERphasing

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    Ministry of Science and Technology (China)China2018YFC1004500
    National Natural Science Foundation of ChinaChinathe Thousand Young Talents Program
    National Natural Science Foundation of ChinaChina31800619

    Revision History 

    • Version 1.0: 2019-08-07
      Type: Initial release
    • Version 1.1: 2020-01-22
      Changes: Database references