4FO6

Crystal structure of the pre-catalytic ternary complex of polymerase lambda with a dATP analog opposite a templating T and an rCMP at the primer terminus.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report



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: 1-10

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

  • 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 ho ...

    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

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA polymerase lambdaA329Homo sapiensMutation(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)
Explore Q9UGP5 
Go to UniProtKB:  Q9UGP5
NIH Common Fund Data Resources
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'T11N/A
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*CP*AP*GP*TP*AP)-R(P*C)-3'P6N/A
      • Find similar nucleic acids by:  Sequence   |   Structure
      • Entity ID: 4
        MoleculeChainsLengthOrganismImage
        5'-D(P*GP*CP*CP*G)-3'D4N/A
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        • Entity ID: 5
          MoleculeChainsLengthOrganismImage
          5'-D(P*TP*AP*CP*TP*G)-3'H5N/A
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          • Entity ID: 6
            MoleculeChainsLengthOrganismImage
            5'-D(P*CP*AP*GP*TP*A)-3'I5N/A
            Small Molecules
            Ligands 5 Unique
            IDChainsName / Formula / InChI Key2D Diagram3D Interactions
            F2A
            Query on F2A

            Download Ideal Coordinates CCD File 
            A
            2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine
            C11 H18 N5 O11 P3
            XETARULVTCYJAN-XLPZGREQSA-N
             Ligand Interaction
            MN
            Query on MN

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            A
            MANGANESE (II) ION
            Mn
            WAEMQWOKJMHJLA-UHFFFAOYSA-N
             Ligand Interaction
            CL
            Query on CL

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            A
            CHLORIDE ION
            Cl
            VEXZGXHMUGYJMC-UHFFFAOYSA-M
             Ligand Interaction
            MG
            Query on MG

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            A
            MAGNESIUM ION
            Mg
            JLVVSXFLKOJNIY-UHFFFAOYSA-N
             Ligand Interaction
            NA
            Query on NA

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

            Experimental Data

            • Method: X-RAY DIFFRACTION
            • Resolution: 2.01 Å
            • R-Value Free: 0.231 
            • R-Value Work: 0.190 
            • R-Value Observed: 0.192 
            • Space Group: P 21 21 21
            Unit Cell:
            Length ( Å )Angle ( ˚ )
            a = 55.78α = 90
            b = 63.655β = 90
            c = 141.47γ = 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 

            • Version 1.0: 2012-07-11
              Type: Initial release