3C5F

Structure of a binary complex of the R517A Pol lambda mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Substrate-induced DNA strand misalignment during catalytic cycling by DNA polymerase lambda.

Bebenek, K.Garcia-Diaz, M.Foley, M.C.Pedersen, L.C.Schlick, T.Kunkel, T.A.

(2008) EMBO Rep 9: 459-464

  • DOI: 10.1038/embor.2008.33
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The simple deletion of nucleotides is common in many organisms. It can be advantageous when it activates genes beneficial to microbial survival in adverse environments, and deleterious when it mutates genes relevant to survival, cancer or degenerativ ...

    The simple deletion of nucleotides is common in many organisms. It can be advantageous when it activates genes beneficial to microbial survival in adverse environments, and deleterious when it mutates genes relevant to survival, cancer or degenerative diseases. The classical idea is that simple deletions arise by strand slippage. A prime opportunity for slippage occurs during DNA synthesis, but it remains unclear how slippage is controlled during a polymerization cycle. Here, we report crystal structures and molecular dynamics simulations of mutant derivatives of DNA polymerase lambda bound to a primer-template during strand slippage. Relative to the primer strand, the template strand is in multiple conformations, indicating intermediates on the pathway to deletion mutagenesis. Consistent with these intermediates, the mutant polymerases generate single-base deletions at high rates. The results indicate that dNTP-induced template strand repositioning during conformational rearrangements in the catalytic cycle is crucial to controlling the rate of strand slippage.


    Organizational Affiliation

    Laboratory of Structural Biology and Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, North Carolina 27709, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA polymerase lambda
A, B
335N/AMutation(s): 1 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
Find proteins for Q9UGP5 (Homo sapiens)
Go to UniProtKB:  Q9UGP5
NIH Common Fund Data Resources
PHAROS  Q9UGP5
Protein Feature View
  • Reference Sequence
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Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DGP*DGP*DCP*DCP*DGP*DTP*DAP*DCP*DTP*DG)-3')T, U11N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DAP*DGP*DTP*DAP*DC)-3')P, Q6N/A
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*DGP*DCP*DCP*DG)-3')D, E4N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.237α = 90
b = 151.884β = 90
c = 85.635γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description