1B04

STRUCTURE OF THE ADENYLATION DOMAIN OF AN NAD+ DEPENDENT LIGASE

• PDB DOI: https://doi.org/10.2210/pdb1B04/pdb

• Classification: LIGASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli BL21
• Mutation(s): Yes 


• Deposited: 1998-11-16 Released: 1999-11-22 
• Deposition Author(s): Singleton, M.R., Hakansson, K., Timson, D.J., Wigley, D.B.

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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 

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

• PubMed: 10368271 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 71.66 kDa 
• Atom Count: 5,126 
• Modelled Residue Count: 621 
• Deposited Residue Count: 636 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (DNA LIGASE)	A, B	318	Geobacillus stearothermophilus	Mutation(s): 1  Gene Names: LIG EC: 6.5.1.2
UniProt
Find proteins for O87703 (Geobacillus stearothermophilus) Explore O87703  Go to UniProtKB:  O87703

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 = 95.72	α = 90
b = 95.72	β = 90
c = 225.89	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-11-22 
Deposition Author(s): Singleton, M.R., Hakansson, K., Timson, D.J., Wigley, D.B.

Revision History  

• 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