3L2P

Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching Between Two DNA Bound States


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Human DNA Ligase III Recognizes DNA Ends by Dynamic Switching between Two DNA-Bound States.

Cotner-Gohara, E.Kim, I.K.Hammel, M.Tainer, J.A.Tomkinson, A.E.Ellenberger, T.

(2010) Biochemistry 49: 6165-6176

  • DOI: 10.1021/bi100503w
  • Primary Citation of Related Structures:  
    3L2P

  • PubMed Abstract: 
  • Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood ...

    Human DNA ligase III has essential functions in nuclear and mitochondrial DNA replication and repair and contains a PARP-like zinc finger (ZnF) that increases the extent of DNA nick joining and intermolecular DNA ligation, yet the bases for ligase III specificity and structural variation among human ligases are not understood. Here combined crystal structure and small-angle X-ray scattering results reveal dynamic switching between two nick-binding components of ligase III: the ZnF-DNA binding domain (DBD) forms a crescent-shaped surface used for DNA end recognition which switches to a ring formed by the nucleotidyl transferase (NTase) and OB-fold (OBD) domains for catalysis. Structural and mutational analyses indicate that high flexibility and distinct DNA binding domain features in ligase III assist both nick sensing and the transition from nick sensing by the ZnF to nick joining by the catalytic core. The collective results support a "jackknife model" in which the ZnF loads ligase III onto nicked DNA and conformational changes deliver DNA into the active site. This work has implications for the biological specificity of DNA ligases and functions of PARP-like zinc fingers.


    Organizational Affiliation

    Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase 3A579Homo sapiensMutation(s): 0 
Gene Names: LIG3
EC: 6.5.1.1
Find proteins for P49916 (Homo sapiens)
Explore P49916 
Go to UniProtKB:  P49916
NIH Common Fund Data Resources
PHAROS:  P49916
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3'B11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3'C9N/A
      Find similar nucleic acids by:  (by identity cutoff)  |  Structure
      Entity ID: 4
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*CP*CP*AP*GP*TP*CP*CP*GP*AP*CP*GP*AP*CP*GP*CP*AP*TP*CP*CP*CP*G)-3'D22N/A
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      AMP
      Query on AMP

      Download Ideal Coordinates CCD File 
      E [auth A]ADENOSINE MONOPHOSPHATE
      C10 H14 N5 O7 P
      UDMBCSSLTHHNCD-KQYNXXCUSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.00 Å
      • R-Value Free: 0.271 
      • R-Value Work: 0.233 
      • R-Value Observed: 0.235 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 130.149α = 90
      b = 130.149β = 90
      c = 150.431γ = 90
      Software Package:
      Software NamePurpose
      HKL-2000data collection
      SOLVEphasing
      REFMACrefinement
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report



      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2010-07-14
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance