1B04

STRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

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This is version 1.4 of the entry. See complete history


Literature

Structure of the adenylation domain of an NAD+-dependent DNA ligase.

Singleton, M.R.Hakansson, K.Timson, D.J.Wigley, D.B.

(1999) Structure 7: 35-42

  • DOI: https://doi.org/10.1016/s0969-2126(99)80007-0
  • Primary Citation of Related Structures:  
    1B04

  • PubMed Abstract: 

    DNA ligases catalyse phosphodiester bond formation between adjacent bases in nicked DNA, thereby sealing the nick. A key step in the catalytic mechanism is the formation of an adenylated DNA intermediate. The adenyl group is derived from either ATP (in eucaryotes and archaea) or NAD+4 (in bacteria). This difference in cofactor specificity suggests that DNA ligase may be a useful antibiotic target. The crystal structure of the adenylation domain of the NAD+-dependent DNA ligase from Bacillus stearothermophilus has been determined at 2.8 A resolution. Despite a complete lack of detectable sequence similarity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD+-binding site. Comparison of the structure of the NAD+4-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates the manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specificities and functionalities in the different members of this enzyme superfamily.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, South ParksRoad, Oxford OX1 3RE, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PROTEIN (DNA LIGASE)
A, B
318Geobacillus stearothermophilusMutation(s): 1 
Gene Names: LIG
EC: 6.5.1.2
UniProt
Find proteins for O87703 (Geobacillus stearothermophilus)
Explore O87703 
Go to UniProtKB:  O87703
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO87703
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.72α = 90
b = 95.72β = 90
c = 225.89γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-11-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Data collection, Database references
  • Version 1.4: 2024-02-07
    Changes: Data collection