2OWO

Last Stop on the Road to Repair: Structure of E.coli DNA Ligase Bound to Nicked DNA-Adenylate

• PDB DOI: https://doi.org/10.2210/pdb2OWO/pdb
• NAKB: 2OWO

• Classification: LIGASE/DNA
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-02-16 Released: 2007-05-15 
• Deposition Author(s): Shuman, S., Nandakumar, J., Nair, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 

Starting Models: experimental

Literature

Last Stop on the Road to Repair: Structure of E. coli DNA Ligase Bound to Nicked DNA-Adenylate.

Nandakumar, J., Nair, P.A., Shuman, S.

(2007) Mol Cell 26: 257-271

• PubMed: 17466627 
• DOI: https://doi.org/10.1016/j.molcel.2007.02.026
• Primary Citation of Related Structures:  
  2OWO


• PubMed Abstract: 
  

  NAD(+)-dependent DNA ligases (LigA) are ubiquitous in bacteria and essential for growth. Their distinctive substrate specificity and domain organization vis-a-vis human ATP-dependent ligases make them outstanding targets for anti-infective drug discovery. We report here the 2.3 A crystal structure of Escherichia coli LigA bound to an adenylylated nick, which captures LigA in a state poised for strand closure and reveals the basis for nick recognition. LigA envelopes the DNA within a protein clamp. Large protein domain movements and remodeling of the active site orchestrate progression through the three chemical steps of the ligation reaction. The structure inspires a strategy for inhibitor design.

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Organizational Affiliation: 

Molecular Biology Program, Sloan-Kettering Institute, New York, NY 10021, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 90.46 kDa 
• Atom Count: 5,991 
• Modelled Residue Count: 638 
• Deposited Residue Count: 723 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	D [auth A]	671	Escherichia coli K-12	Mutation(s): 0  Gene Names: ligA EC: 6.5.1.2
UniProt
Find proteins for P15042 (Escherichia coli (strain K12)) Explore P15042  Go to UniProtKB:  P15042

Entity ID: 1
Molecule	Chains	Length	Organism	Image
26-MER	A [auth B]	26	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*AP*CP*AP*AP*TP*TP*GP*CP*GP*AP*CP*(OMC)P*C)-3'	B [auth C]	13	N/A

Entity ID: 3
Molecule	Chains	Length	Organism	Image
5'-D(*CP*AP*CP*TP*AP*TP*CP*GP*GP*AP*AP*TP*G)-3'	C [auth D]	13	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	E [auth D]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	G [auth A], H [auth A], I [auth A], J [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	F [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.254 
• R-Value Work: 0.217 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.441	α = 90
b = 99.273	β = 105.33
c = 86.245	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-15 
Deposition Author(s): Shuman, S., Nandakumar, J., Nair, P.A.

Revision History  

• Version 1.0: 2007-05-15
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description