Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 74.22 kDa 
• Atom Count: 5499 
• Modelled Residue Count: 616 
• Deposited Residue Count: 636 
• Unique protein chains: 1

3JSL

Crystal structure of the adenylation domain of NAD+-dependent DNA ligase from Staphylococcus aureus

• DOI: 10.2210/pdb3JSL/pdb

• Classification: LIGASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-10 Released: 2009-12-15 
• Deposition Author(s): Han, S., Chang, J.S., Griffor, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.250 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 

Literature

Structure of the adenylation domain of NAD(+)-dependent DNA ligase from Staphylococcus aureus.

Han, S., Chang, J.S., Griffor, M.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 1078-1082

• PubMed: 19923722 
• DOI: 10.1107/S1744309109036872
• Primary Citation of Related Structures:  
  3JSL, 3JSN


• PubMed Abstract: 
  

DNA ligase catalyzes phosphodiester-bond formation between immediately adjacent 5'-phosphate and 3'-hydroxyl groups in double-stranded DNA and plays a central role in many cellular and biochemical processes, including DNA replication, repair and recombination. Bacterial NAD(+)-dependent DNA ligases have been extensively characterized as potential antibacterial targets because of their essentiality and their structural distinction from human ATP-dependent DNA ligases. The high-resolution structure of the adenylation domain of Staphylococcus aureus NAD(+)-dependent DNA ligase establishes the conserved domain architecture with other bacterial adenylation domains. Two apo crystal structures revealed that the active site possesses the preformed NAD(+)-binding pocket and the 'C2 tunnel' lined with hydrophobic residues: Leu80, Phe224, Leu287, Phe295 and Trp302. The C2 tunnel is unique to bacterial DNA ligases and the Leu80 side chain at the mouth of the tunnel points inside the tunnel and forms a narrow funnel in the S. aureus DNA ligase structure. Taken together with other DNA ligase structures, the S. aureus DNA ligase structure provides a basis for a more integrated understanding of substrate recognition and catalysis and will be also be of help in the development of small-molecule inhibitors.

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Organizational Affiliation: 

Pfizer Inc., Groton, Connecticut 06340, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A, B	318	Staphylococcus aureus	Mutation(s): 0  Gene Names: ligA, lig EC: 6.5.1.2
UniProt
Find proteins for Q9AIU7 (Staphylococcus aureus) Explore Q9AIU7  Go to UniProtKB:  Q9AIU7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.250 
• R-Value Work: 0.196 
• R-Value Observed: 0.198 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.152	α = 90.1
b = 49.193	β = 103.2
c = 88.039	γ = 90.01

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-09-10 
• Released Date: 2009-12-15 
Deposition Author(s): Han, S., Chang, J.S., Griffor, M.

Revision History  

• Version 1.0: 2009-12-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance