1XSN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 

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
  • Primary Citation of Related Structures:  

  • 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: 
    • 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
    • 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
    • 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
    • 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


    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
335Homo sapiensMutation(s): 1 
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(*CP*GP*GP*CP*AP*AP*TP*AP*CP*TP*G)-3'T11N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*AP*GP*TP*AP*(2DT))-3'P6N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(P*GP*CP*CP*G)-3'D4N/A
Small Molecules
Ligands 4 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
EDO
Query on EDO

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Download CCD File 
P, T
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
D3T
Query on D3T

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Download CCD File 
A
2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
C10 H17 N2 O13 P3
URGJWIFLBWJRMF-JGVFFNPUSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
2DT
Query on 2DT
P
DNA LINKINGC10 H15 N2 O7 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.043α = 90.00
b = 62.551β = 90.00
c = 139.830γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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