3MGH

Binary complex of a DNA polymerase lambda loop mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Loop 1 modulates the fidelity of DNA polymerase lambda

Bebenek, K.Garcia-Diaz, M.Zhou, R.Z.Povirk, L.F.Kunkel, T.A.

(2010) Nucleic Acids Res. 38: 5419-5431

  • DOI: 10.1093/nar/gkq261
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Differences in the substrate specificity of mammalian family X DNA polymerases are proposed to partly depend on a loop (loop 1) upstream of the polymerase active site. To examine if this is the case in DNA polymerase λ (pol λ), here we characterize a ...

    Differences in the substrate specificity of mammalian family X DNA polymerases are proposed to partly depend on a loop (loop 1) upstream of the polymerase active site. To examine if this is the case in DNA polymerase λ (pol λ), here we characterize a variant of the human polymerase in which nine residues of loop 1 are replaced with four residues from the equivalent position in pol β. Crystal structures of the mutant enzyme bound to gapped DNA with and without a correct dNTP reveal that the change in loop 1 does not affect the overall structure of the protein. Consistent with these structural data, the mutant enzyme has relatively normal catalytic efficiency for correct incorporation, and it efficiently participates in non-homologous end joining of double-strand DNA breaks. However, DNA junctions recovered from end-joining reactions are more diverse than normal, and the mutant enzyme is substantially less accurate than wild-type pol λ in three different biochemical assays. Comparisons of the binary and ternary complex crystal structures of mutant and wild-type pol λ suggest that loop 1 modulates pol λ's fidelity by controlling dNTP-induced movements of the template strand and the primer-terminal 3'-OH as the enzyme transitions from an inactive to an active conformation.


    Organizational Affiliation

    Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase lambda
A, C
329Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7, 4.2.99.-
Find proteins for Q9UGP5 (Homo sapiens)
Go to Gene View: POLL
Go to UniProtKB:  Q9UGP5
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*GP*CP*AP*GP*TP*AP*CP*TP*G)-3')T,E11N/A
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*AP*GP*TP*AP*C)-3')P,F6N/A
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*CP*CP*G)-3')D,G4N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.998α = 90.00
b = 190.886β = 90.00
c = 58.734γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
DENZOdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-05-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-07-26
    Type: Data collection, Refinement description, Source and taxonomy
  • Version 1.3: 2017-11-08
    Type: Refinement description