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 

wwPDB Validation 3D Report Full Report


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
  • Structures With Same Primary Citation

  • 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 ...

    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 LengthOrganismDetails
DNA ligase I
A
688Homo sapiensMutation(s): 6 
Gene Names: LIG1
EC: 6.5.1.1
Find proteins for P18858 (Homo sapiens)
Go to UniProtKB:  P18858
NIH Common Fund Data Resources
PHAROS  P18858
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Entity ID: 1
MoleculeChainsLengthOrganism
dideoxy terminated DNAB13N/A
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Entity ID: 2
MoleculeChainsLengthOrganism
5'-phosphorylated DNAC15N/A

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Entity ID: 3
MoleculeChainsLengthOrganism
template DNAD28N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download CCD File 
C
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
AL-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 

  • 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