1A0I | pdb_00001a0i

ATP-DEPENDENT DNA LIGASE FROM BACTERIOPHAGE T7 COMPLEX WITH ATP

• PDB DOI: https://doi.org/10.2210/pdb1A0I/pdb

• Classification: LIGASE
• Organism(s): Escherichia phage T7
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-12-01 Released: 1998-03-25 
• Deposition Author(s): Subramanya, H.S., Doherty, A.J., Ashford, S.R., Wigley, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.341 (Depositor), 0.325 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.213 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.

Subramanya, H.S., Doherty, A.J., Ashford, S.R., Wigley, D.B.

(1996) Cell 85: 607-615

• PubMed: 8653795 
• DOI: https://doi.org/10.1016/s0092-8674(00)81260-x
• Primary Citation Related Structures: 
  1A0I


• PubMed Abstract: 
  

  The crystal structure of the ATP-dependent DNA ligase from bacteriophage T7 has been solved at 2.6 A resolution. The protein comprises two domains with a deep cleft running between them. The structure of a complex with ATP reveals that the nucleotide binding pocket is situated on the larger N-terminal domain, at the base of the cleft between the two domains of the enzyme. Comparison of the overall domain structure with that of DNA methyltransferases, coupled with other evidence, suggests that DNA also binds in this cleft. Since this structure is the first of the nucleotidyltransferase superfamily, which includes the eukaryotic mRNA capping enzymes, the relationship between the structure of DNA ligase and that of other nucleotidyltransferases is also discussed.

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Organizational Affiliation: 
• Laboratory of Molecular Biophysics, University of Oxford, United Kingdom.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 40.4 kDa 
• Atom Count: 2,903 
• Modeled Residue Count: 332 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA LIGASE	A	348	Escherichia phage T7	Mutation(s): 0  Gene Names: LIG EC: 6.5.1.1
UniProt
Find proteins for P00969 (Escherichia phage T7) Explore P00969  Go to UniProtKB:  P00969

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	B [auth A]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.341 (Depositor), 0.325 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.213 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.7	α = 90
b = 85.2	β = 90
c = 79.1	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-03-25 
Deposition Author(s): Subramanya, H.S., Doherty, A.J., Ashford, S.R., Wigley, D.B.

Revision History  

• Version 1.0: 1998-03-25
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-07
  Changes: Data collection, Database references, Derived calculations, Other