1FVI | pdb_00001fvi

CRYSTAL STRUCTURE OF CHLORELLA VIRUS DNA LIGASE-ADENYLATE

• PDB DOI: https://doi.org/10.2210/pdb1FVI/pdb

• Classification: LIGASE
• Organism(s): Chlorella virus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2000-09-20 Released: 2000-11-22 
• Deposition Author(s): Odell, M., Sriskanda, V., Shuman, S., Nikolov, D.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.270 (Depositor) 
• R-Value Work: 
  0.190 (Depositor) 

Literature

Crystal structure of eukaryotic DNA ligase-adenylate illuminates the mechanism of nick sensing and strand joining.

Odell, M., Sriskanda, V., Shuman, S., Nikolov, D.B.

(2000) Mol Cell 6: 1183-1193

• PubMed: 11106756 
• DOI: https://doi.org/10.1016/s1097-2765(00)00115-5
• Primary Citation Related Structures: 
  1FVI


• PubMed Abstract: 
  

  Chlorella virus DNA ligase is the smallest eukaryotic ATP-dependent ligase known; it has an intrinsic nick-sensing function and suffices for yeast cell growth. Here, we report the 2.0 A crystal structure of the covalent ligase-AMP reaction intermediate. The conformation of the adenosine nucleoside and contacts between the enzyme and the ribose sugar have undergone a significant change compared to complexes of T7 ligase with ATP or mRNA capping enzyme with GTP. The conformational switch allows the 3' OH of AMP to coordinate directly the 5' PO(4) of the nick. The structure explains why nick sensing is restricted to adenylated ligase and why the 5' phosphate is required for DNA binding. We identify a metal binding site on ligase-adenylate and propose a mechanism of nick recognition and catalysis supported by mutational data.

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Organizational Affiliation: 
• Molecular Biology Program and Cellular Biochemistry and Biophysics 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: 34.57 kDa 
• Atom Count: 2,430 
• Modeled Residue Count: 264 
• Deposited Residue Count: 297 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CHLORELLA VIRUS DNA LIGASE-ADENYLATE	A	297	Chlorella virus	Mutation(s): 1  EC: 6.5.1
UniProt
Find proteins for A0ACD6B8E9 (Paramecium bursaria Chlorella virus AR158) Explore A0ACD6B8E9  Go to UniProtKB:  A0ACD6B8E9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
SO4	B [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.270 (Depositor) 
• R-Value Work:  0.190 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.17	α = 90
b = 58.44	β = 90
c = 101.79	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-11-22 
Deposition Author(s): Odell, M., Sriskanda, V., Shuman, S., Nikolov, D.B.

Revision History  

• Version 1.0: 2000-11-22
  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: Database references, Derived calculations
• Version 1.4: 2024-11-20
  Changes: Data collection, Structure summary