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
  • Primary Citation of Related Structures:  
    1XSL, 1XSN, 1XSP

  • 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 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 ...

    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

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaM [auth A],
N [auth E],
O [auth I],
P [auth M]
335Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5
GTEx:  ENSG00000166169 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UGP5
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
5'-D(*CP*GP*GP*CP*AP*GP*CP*GP*CP*AP*C)-3'A [auth B],
D [auth F],
G [auth J],
J [auth N]
11N/A
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5'-D(*GP*TP*GP*CP*GP*C)-3'B [auth C],
E [auth G],
H [auth K],
K [auth O]
6N/A
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5'-D(P*GP*CP*CP*G)-3'C [auth D],
F [auth H],
I [auth L],
L [auth P]
4N/A
Protein Feature View
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  • Reference Sequence
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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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