1XSL

Crystal Structure of human DNA polymerase lambda in complex with a one nucleotide DNA gap


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A closed conformation for the Pol lambda catalytic cycle.

Garcia-Diaz, M.Bebenek, K.Krahn, J.M.Kunkel, T.A.Pedersen, L.C.

(2005) Nat Struct Mol Biol 12: 97-98

  • DOI: 10.1038/nsmb876
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Pol lambda is a family X member believed to fill short gaps during DNA repair. Here we report crystal structures of Pol lambda representing three steps in filling a single-nucleotide gap. These structures indicate that, unlike other DNA polymerases, ...

    Pol lambda is a family X member believed to fill short gaps during DNA repair. Here we report crystal structures of Pol lambda representing three steps in filling a single-nucleotide gap. These structures indicate that, unlike other DNA polymerases, Pol lambda does not undergo large subdomain movements during catalysis, and they provide a clear characterization of the geometry and stereochemistry of the in-line nucleotidyl transfer reaction.


    Related Citations: 
    • A Structural Solution for the DNA Polymerase-lambda Dependent Repair of DNA Gaps with Minimal Homology
      Garcia-Diaz, M., Bebenek, K., Krahn, J.M., Blanco, L., Kunkel, T.A., Pedersen, L.C.
      (2004) Mol Cell 13: 561
    • DNA polymerase lambda, a novel DNA repair enzyme in human cells
      Garcia-Diaz, M., Bebenek, K., Sabariegos, R., Dominguez, O., Rodriguez, J., Kirchhoff, T., Garcia-Palomero, E., Picher, A.J., Juarez, R., Ruiz, J.F., Kunkel, T.A., Blanco, L.
      (2002) J Biol Chem 277: 13184
    • The frameshift Infidelity of human DNA polymerase lambda. Implications for function.
      Bebenek, K., Garcia-Diaz, K., Blanco, L., Kunkel, T.A.
      (2003) J Biol Chem 278: 34685
    • Identification of an intrinsic 5'-deoxyribose-5-phosphate lyase activity in human DNA polymerase lambda: a possible role in Base Excision Repair
      Garcia-Diaz, M., Bebenek, K., Kunkel, T.A., Blanco, L.
      (2001) J Biol Chem 276: 34659

    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase lambda
A, E, I, M
335Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (UniProt)
Find proteins for Q9UGP5 (Homo sapiens)
Go to UniProtKB:  Q9UGP5
NIH Common Fund Data Resources
PHAROS  Q9UGP5
Protein Feature View
  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'B, F,J,N11N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*TP*GP*CP*GP*C)-3'C, G,K,O6N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(P*GP*CP*CP*G)-3'D, H,L,P4N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CAC
Query on CAC

Download CCD File 
D
CACODYLATE ION
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download CCD File 
B, F, H
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, E, I, J, M, N
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 191.504α = 90
b = 98.812β = 90
c = 104.519γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-01-18
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-24
    Changes: Database references