2BCV

DNA polymerase lambda in complex with Dttp and a DNA duplex containing an unpaired Dtmp


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural analysis of strand misalignment during DNA synthesis by a human DNA polymerase

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

(2006) Cell 124: 331-342

  • DOI: 10.1016/j.cell.2005.10.039
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Insertions and deletions in coding sequences can alter the reading frame of genes and have profound biological consequences. In 1966, Streisinger proposed that these mutations result from strand slippage, which in repetitive sequences generates misal ...

    Insertions and deletions in coding sequences can alter the reading frame of genes and have profound biological consequences. In 1966, Streisinger proposed that these mutations result from strand slippage, which in repetitive sequences generates misaligned intermediates stabilized by correct base pairing that support polymerization. We report here crystal structures of human DNA polymerase lambda, which frequently generates deletion mutations, bound to such intermediates. Each contains an extrahelical template nucleotide upstream of the active site. Surprisingly, the extra nucleotide, even when combined with an adjacent mismatch, does not perturb polymerase active site geometry, which is indistinguishable from that for correctly aligned strands. These structures reveal how pol lambda can polymerize on substrates with minimal homology during repair of double-strand breaks and represent strand-slippage intermediates consistent with Streisinger's classical hypothesis. They are thus relevant to the origin of single-base deletions, a class of mutations that can confer strong biological phenotypes.


    Organizational Affiliation

    Laboratory of Structural Biology, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase lambda
A
335Homo 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: 1
MoleculeChainsLengthOrganism
5'-D(P*GP*CP*CP*G)-3'D4N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*AP*GP*TP*AP*(O2C))-3'P6N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*CP*GP*GP*CP*AP*GP*TP*TP*AP*CP*TP*G)-3'T12N/A
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
TTP
Query on TTP

Download SDF File 
Download CCD File 
A
THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O14 P3
NHVNXKFIZYSCEB-XLPZGREQSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
O2C
Query on O2C
P
RNA LINKINGC9 H14 N3 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 55.140α = 90.00
b = 62.988β = 90.00
c = 141.936γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALEPACKdata scaling
CNSrefinement
STRUCTUREdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-03-07
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance