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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 (s ...

    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 Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA. brandt.eichman@vanderbilt.edu.,Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA. brandt.eichman@vanderbilt.edu.,Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA. david.cortez@vanderbilt.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SOS response-associated peptidase YedK
A, B
227Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: yedK (yedG)
EC: 3.4.-.-
Find proteins for P76318 (Escherichia coli (strain K12))
Go to UniProtKB:  P76318
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*TP*CP*(PED)P*GP*GP*A)-3')C,D7Escherichia coli
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PED
Query on PED
C, D
NON-POLYMERC5 H13 O6 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.171 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.258α = 90.00
b = 41.886β = 95.78
c = 81.423γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01GM117299
National Institutes of Health/National Human Genome Research InstituteUnited StatesP01CA092584

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-10
    Type: Data collection, Database references
  • Version 1.2: 2019-07-17
    Type: Data collection, Database references