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 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 

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

  • 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 II ...

    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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase 3
A
579Homo sapiensGene Names: LIG3
EC: 6.5.1.1
Find proteins for P49916 (Homo sapiens)
Go to Gene View: LIG3
Go to UniProtKB:  P49916
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(P*CP*GP*GP*GP*AP*TP*GP*CP*GP*TP*C)-3'B11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*TP*CP*GP*GP*AP*CP*TP*G)-3'C9N/A
Entity ID: 4
MoleculeChainsLengthOrganism
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 SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.233 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 130.149α = 90.00
b = 130.149β = 90.00
c = 150.431γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
SOLVEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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