1X9N

Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

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This is version 1.2 of the entry. See complete history


Literature

Human DNA ligase I completely encircles and partially unwinds nicked DNA.

Pascal, J.M.O'Brien, P.J.Tomkinson, A.E.Ellenberger, T.

(2004) Nature 432: 473-478

  • DOI: 10.1038/nature03082
  • Primary Citation of Related Structures:  
    1X9N

  • PubMed Abstract: 
  • The end-joining reaction catalysed by DNA ligases is required by all organisms and serves as the ultimate step of DNA replication, repair and recombination processes. One of three well characterized mammalian DNA ligases, DNA ligase I, joins Okazaki fragments during DNA replication ...

    The end-joining reaction catalysed by DNA ligases is required by all organisms and serves as the ultimate step of DNA replication, repair and recombination processes. One of three well characterized mammalian DNA ligases, DNA ligase I, joins Okazaki fragments during DNA replication. Here we report the crystal structure of human DNA ligase I (residues 233 to 919) in complex with a nicked, 5' adenylated DNA intermediate. The structure shows that the enzyme redirects the path of the double helix to expose the nick termini for the strand-joining reaction. It also reveals a unique feature of mammalian ligases: a DNA-binding domain that allows ligase I to encircle its DNA substrate, stabilizes the DNA in a distorted structure, and positions the catalytic core on the nick. Similarities in the toroidal shape and dimensions of DNA ligase I and the proliferating cell nuclear antigen sliding clamp are suggestive of an extensive protein-protein interface that may coordinate the joining of Okazaki fragments.


    Organizational Affiliation

    Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA ligase ID [auth A]688Homo sapiensMutation(s): 6 
Gene Names: LIG1
EC: 6.5.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P18858 (Homo sapiens)
Explore P18858 
Go to UniProtKB:  P18858
PHAROS:  P18858
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    dideoxy terminated DNAA [auth B]13N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-phosphorylated DNAB [auth C]15N/A
      Protein Feature View
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      • Reference Sequence
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      Entity ID: 3
      MoleculeChainsLengthOrganismImage
      template DNAC [auth D]28N/A
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 1 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      AMP
      Query on AMP

      Download Ideal Coordinates CCD File 
      E [auth C]ADENOSINE MONOPHOSPHATE
      C10 H14 N5 O7 P
      UDMBCSSLTHHNCD-KQYNXXCUSA-N
       Ligand Interaction
      Modified Residues  1 Unique
      IDChainsTypeFormula2D DiagramParent
      MSE
      Query on MSE
      D [auth A]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.00 Å
      • R-Value Free: 0.268 
      • R-Value Work: 0.235 
      • R-Value Observed: 0.236 
      • Space Group: P 63
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 161.889α = 90
      b = 161.889β = 90
      c = 88.455γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      ACEdata reduction
      HKL-2000data scaling
      SHARPphasing

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2004-11-30
        Type: Initial release
      • Version 1.1: 2008-04-30
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Advisory, Version format compliance