1V9P | pdb_00001v9p

Crystal Structure Of Nad+-Dependent DNA Ligase

• PDB DOI: https://doi.org/10.2210/pdb1V9P/pdb
• Entry: 1V9P supersedes: 1DGT

• Classification: LIGASE
• Organism(s): Thermus filiformis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-01-27 Released: 2004-03-30 
• Deposition Author(s): Lee, J.Y., Chang, C., Song, H.K., Moon, J., Yang, J.K., Kim, H.K., Kwon, S.K., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.293 (Depositor), 0.303 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.244 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Literature

Crystal structure of NAD(+)-dependent DNA ligase: modular architecture and functional implications.

Lee, J.Y., Chang, C., Song, H.K., Moon, J., Yang, J.K., Kim, H.K., Kwon, S.T., Suh, S.W.

(2000) EMBO J 19: 1119-1129

• PubMed: 10698952 
• DOI: https://doi.org/10.1093/emboj/19.5.1119
• Primary Citation Related Structures: 
  1DGS, 1V9P


• PubMed Abstract: 
  

  DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor. Despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of DNA ligase share basically the same catalytic mechanism. In this study, the crystal structure of an NAD(+)-dependent DNA ligase from Thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwavelength anomalous diffraction (MAD) method. It reveals highly modular architecture and a unique circular arrangement of its four distinct domains. It also provides clues for protein flexibility and DNA-binding sites. A model for the multidomain ligase action involving large conformational changes is proposed.

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Organizational Affiliation: 
• Center for Molecular Catalysis, Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-742.

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: 135.47 kDa 
• Atom Count: 9,768 
• Modeled Residue Count: 1,168 
• Deposited Residue Count: 1,168 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA ligase	A, B	584	Thermus filiformis	Mutation(s): 0  Gene Names: LIGA EC: 6.5.1.2
UniProt
Find proteins for Q9ZHI0 (Thermus filiformis) Explore Q9ZHI0  Go to UniProtKB:  Q9ZHI0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	D [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.293 (Depositor), 0.303 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.244 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.21	α = 90
b = 117.33	β = 115.09
c = 97.48	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-03-30 
Deposition Author(s): Lee, J.Y., Chang, C., Song, H.K., Moon, J., Yang, J.K., Kim, H.K., Kwon, S.K., Suh, S.W.
• This entry supersedes: 1DGT

Revision History  

• Version 1.0: 2004-03-30
  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: 2023-12-27
  Changes: Data collection, Database references, Derived calculations