1DGS

CRYSTAL STRUCTURE OF NAD+-DEPENDENT DNA LIGASE FROM T. FILIFORMIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.228 

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This is version 1.2 of the entry. See complete history


Literature

Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.

Lee, J.Y.Chang, C.Song, H.K.Moon, J.Yang, J.K.Kim, H.K.Kwon, S.T.Suh, S.W.

(2000) EMBO J 19: 1119-1129

  • DOI: https://doi.org/10.1093/emboj/19.5.1119
  • Primary Citation of Related Structures:  
    1DGS, 1V9P

  • PubMed Abstract: 

    DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.


  • Organizational Affiliation

    Center for Molecular Catalysis, Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA LIGASE
A, B
667Thermus filiformisMutation(s): 0 
EC: 6.5.1.2
UniProt
Find proteins for Q9ZHI0 (Thermus filiformis)
Explore Q9ZHI0 
Go to UniProtKB:  Q9ZHI0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZHI0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.21α = 90
b = 117.33β = 115.09
c = 97.48γ = 90
Software Package:
Software NamePurpose
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-11-27
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance