3UQ0

Crystal structure of the post-catalytic product complex of polymerase lambda with an rAMP at the primer terminus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.14 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The catalytic cycle for ribonucleotide incorporation by human DNA Pol lambda

Gosavi, R.A.Moon, A.F.Kunkel, T.A.Pedersen, L.C.Bebenek, K.

(2012) Nucleic Acids Res 40: 7518-7527

  • DOI: 10.1093/nar/gks413
  • Primary Citation of Related Structures:  
    3UQ0, 3UPQ, 3UQ2, 4FO6

  • PubMed Abstract: 
  • Although most DNA polymerases discriminate against ribonucleotide triphosphaets (rNTPs) during DNA synthesis, recent studies have shown that large numbers of ribonucleotides are incorporated into the eukaryotic nuclear genome. Here, we investigate how a DNA polymerase can stably incorporate an rNTP ...

    Although most DNA polymerases discriminate against ribonucleotide triphosphaets (rNTPs) during DNA synthesis, recent studies have shown that large numbers of ribonucleotides are incorporated into the eukaryotic nuclear genome. Here, we investigate how a DNA polymerase can stably incorporate an rNTP. The X-ray crystal structure of a variant of human DNA polymerase λ reveals that the rNTP occupies the nucleotide binding pocket without distortion of the active site, despite an unfavorable interaction between the 2'-O and Tyr505 backbone carbonyl. This indicates an energetically unstable binding state for the rNTP, stabilized by additional protein-nucleotide interactions. Supporting this idea is the 200-fold lower catalytic efficiency for rNTP relative to deoxyribonucleotide triphosphate (dNTP) incorporation, reflecting a higher apparent Km value for the rNTP. Furthermore, distortion observed in the structure of the post-catalytic product complex suggests that once the bond between the α- and β-phosphates of the rNTP is broken, the unfavorable binding state of the ribonucleotide cannot be maintained. Finally, structural and biochemical evaluation of dNTP insertion onto an ribonucleotide monophosphate (rNMP)-terminated primer indicates that a primer-terminal rNMP does not impede extension. The results are relevant to how ribonucleotides are incorporated into DNA in vivo, during replication and during repair, perhaps especially in non-proliferating cells when rNTP:dNTP ratios are high.


    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, NC, 27709, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaA329Homo sapiensMutation(s): 0 
Gene Names: POLL
EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UGP5 (Homo sapiens)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
PHAROS:  Q9UGP5
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*GP*CP*TP*GP*TP*AP*CP*TP*G)-3'B [auth T]11N/A
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*GP*TP*AP*CP)-R(P*A)-3'C [auth P]7N/A
      Protein Feature View
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      • Reference Sequence
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      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*CP*CP*G)-3'D4N/A
        Protein Feature View
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        • Reference Sequence
        Experimental Data & Validation

        Experimental Data

        • Method: X-RAY DIFFRACTION
        • Resolution: 2.14 Å
        • R-Value Free: 0.239 
        • R-Value Work: 0.195 
        • R-Value Observed: 0.197 
        • Space Group: P 21 21 21
        Unit Cell:
        Length ( Å )Angle ( ˚ )
        a = 55.843α = 90
        b = 64.241β = 90
        c = 139.29γ = 90
        Software Package:
        Software NamePurpose
        HKL-2000data collection
        PHENIXmodel building
        PHENIXrefinement
        HKL-2000data reduction
        HKL-2000data scaling
        PHENIXphasing

        Structure Validation

        View Full Validation Report



        Entry History 

        Deposition Data

        Revision History  (Full details and data files)

        • Version 1.0: 2012-05-23
          Type: Initial release
        • Version 1.1: 2012-07-18
          Changes: Database references
        • Version 1.2: 2012-09-26
          Changes: Database references