6NUA

DNA-protein crosslink between E. coli YedK and ssDNA containing an abasic site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Protection of abasic sites during DNA replication by a stable thiazolidine protein-DNA cross-link.

Thompson, P.S.Amidon, K.M.Mohni, K.N.Cortez, D.Eichman, B.F.

(2019) Nat Struct Mol Biol 26: 613-618

  • DOI: 10.1038/s41594-019-0255-5
  • Primary Citation of Related Structures:  
    6NUH, 6NUA

  • PubMed Abstract: 
  • Abasic (AP) sites are one of the most common DNA lesions that block replicative polymerases. 5-hydroxymethylcytosine binding, embryonic stem cell-specific protein (HMCES) recognizes and processes these lesions in the context of single-stranded DNA (ssDNA ...

    Abasic (AP) sites are one of the most common DNA lesions that block replicative polymerases. 5-hydroxymethylcytosine binding, embryonic stem cell-specific protein (HMCES) recognizes and processes these lesions in the context of single-stranded DNA (ssDNA). A HMCES DNA-protein cross-link (DPC) intermediate is thought to shield the AP site from endonucleases and error-prone polymerases. The highly evolutionarily conserved SOS-response associated peptidase (SRAP) domain of HMCES and its Escherichia coli ortholog YedK mediate lesion recognition. Here we uncover the basis of AP site protection by SRAP domains from a crystal structure of the YedK DPC. YedK forms a stable thiazolidine linkage between a ring-opened AP site and the α-amino and sulfhydryl substituents of its amino-terminal cysteine residue. The thiazolidine linkage explains the remarkable stability of the HMCES DPC, its resistance to strand cleavage and the proteolysis requirement for resolution. Furthermore, its structure reveals that HMCES has specificity for AP sites in ssDNA at junctions found when replicative polymerases encounter the AP lesion.


    Organizational Affiliation

    Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. brandt.eichman@vanderbilt.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SOS response-associated peptidase YedK AB227Escherichia coliMutation(s): 0 
Gene Names: yedKyedGb1931JW1916
EC: 3.4
Find proteins for P76318 (Escherichia coli (strain K12))
Explore P76318 
Go to UniProtKB:  P76318
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3')C, D7Escherichia coli
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.64 Å
    • R-Value Free: 0.222 
    • R-Value Work: 0.171 
    • R-Value Observed: 0.173 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 61.258α = 90
    b = 41.886β = 95.78
    c = 81.423γ = 90
    Software Package:
    Software NamePurpose
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing
    PHENIXrefinement
    PDB_EXTRACTdata extraction

    Structure Validation

    View Full Validation Report



    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesR01GM117299
    National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP01CA092584

    Revision History 

    • Version 1.0: 2019-06-26
      Type: Initial release
    • Version 1.1: 2019-07-10
      Changes: Data collection, Database references
    • Version 1.2: 2019-07-17
      Changes: Data collection, Database references
    • Version 1.3: 2019-12-18
      Changes: Author supporting evidence