6NUH

Non-covalent DNA-protein complex between E. coli YedK and ssDNA containing an abasic site analog

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.177 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.4 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 A226Escherichia coliMutation(s): 0 
Gene Names: yedK, yedG, b1931, JW1916
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*(PDI)P*GP*GP*A)-3')C7Escherichia coli
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    BTB
    Query on BTB
    Download Ideal Coordinates CCD File 
    A
    		2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
    C8 H19 N O5
    OWMVSZAMULFTJU-UHFFFAOYSA-N    		 Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.59 Å
    • R-Value Free: 0.177 
    • R-Value Work: 0.143 
    • R-Value Observed: 0.145 
    • Space Group: P 1 21 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 47.543α = 90
    b = 44.129β = 102.34
    c = 55.093γ = 90
    Software Package:
    Software NamePurpose
    PHENIXrefinement
    HKL-2000data reduction
    HKL-2000data scaling
    PHASERphasing

    Structure Validation

    View Full Validation Report


    View more in-depth experimental data

    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: 2019-08-21
      Changes: Data collection, Structure summary
    • Version 1.4: 2019-12-18
      Changes: Author supporting evidence