6KBS

Crystal structure of yedK in complex with ssDNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

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_04370D9J52_16500GHR40_13845GQE34_17870
EC: 3.4
Find proteins for A0A2S5ZH06 (Escherichia coli)
Explore A0A2S5ZH06 
Go to UniProtKB:  A0A2S5ZH06
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*GP*TP*CP*GP*AP*TP*TP*C)-3')D10Escherichia coli
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.60 Å
    • R-Value Free: 0.201 
    • R-Value Work: 0.173 
    • R-Value Observed: 0.174 
    • Space Group: C 1 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 91.89α = 90
    b = 50.322β = 99.08
    c = 54.531γ = 90
    Software Package:
    Software NamePurpose
    SCALEPACKdata scaling
    PHENIXrefinement
    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: 2019-07-10
      Type: Initial release
    • Version 1.1: 2020-01-22
      Changes: Database references