1ZAU

Adenylation domain of NAD+ dependent DNA ligase from M.tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.253 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

NAD+-dependent DNA Ligase (Rv3014c) from Mycobacterium tuberculosis: CRYSTAL STRUCTURE OF THE ADENYLATION DOMAIN AND IDENTIFICATION OF NOVEL INHIBITORS

Srivastava, S.K.Tripathi, R.P.Ramachandran, R.

(2005) J.Biol.Chem. 280: 30273-30281

  • DOI: 10.1074/jbc.M503780200

  • PubMed Abstract: 
  • DNA ligases utilize either ATP or NAD+ as cofactors to catalyze the formation of phosphodiester bonds in nicked DNA. Those utilizing NAD+ are attractive drug targets because of the unique cofactor requirement for ligase activity. We report here the c ...

    DNA ligases utilize either ATP or NAD+ as cofactors to catalyze the formation of phosphodiester bonds in nicked DNA. Those utilizing NAD+ are attractive drug targets because of the unique cofactor requirement for ligase activity. We report here the crystal structure of the adenylation domain of the Mycobacterium tuberculosis NAD+-dependent ligase with bound AMP. The adenosine nucleoside moiety of AMP adopts a syn-conformation. The structure also captures a new spatial disposition between the two subdomains of the adenylation domain. Based on the crystal structure and an in-house compound library, we have identified a novel class of inhibitors for the enzyme using in silico docking calculations. The glycosyl ureide-based inhibitors were able to distinguish between NAD+- and ATP-dependent ligases as evidenced by in vitro assays using T4 ligase and human DNA ligase I. Moreover, assays involving an Escherichia coli strain harboring a temperature-sensitive ligase mutant and a ligase-deficient Salmonella typhimurium strain suggested that the bactericidal activity of the inhibitors is due to inhibition of the essential ligase enzyme. The results can be used as the basis for rational design of novel antibacterial agents.


    Organizational Affiliation

    Division Molecular and Structural Biology, Central Drug Research Institute, Chattar Manzil, Mahatma Gandhi Marg, Lucknow-226001, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA ligase
A
328Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 0 
Gene Names: ligA (lig)
EC: 6.5.1.2
Find proteins for P9WNV1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WNV1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AMP
Query on AMP

Download SDF File 
Download CCD File 
A
ADENOSINE MONOPHOSPHATE
C10 H14 N5 O7 P
UDMBCSSLTHHNCD-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.253 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 95.800α = 90.00
b = 95.800β = 90.00
c = 208.400γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
X-PLORrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-07-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description