4ANE

R80N MUTANT OF NUCLEOSIDE DIPHOSPHATE KINASE FROM MYCOBACTERIUM TUBERCULOSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of Mycobacterium Tuberculosis Nucleoside Diphosphate Kinase R80N Mutant in Complex with Citrate

Georgescauld, F.Moynie, L.Habersetzer, J.Dautant, A.

(2014) Acta Crystallogr.,Sect.D 70: 40

  • DOI: 10.1107/S2053230X13034134

  • PubMed Abstract: 
  • The crystal structure of the wild-type nucleoside diphosphate kinase from Mycobacterium tuberculosis at 2.6 Å resolution revealed that the intersubunit salt bridge Arg80-Asp93 contributes to the thermal stability of the hexamer (Tm = 76°C). On mutati ...

    The crystal structure of the wild-type nucleoside diphosphate kinase from Mycobacterium tuberculosis at 2.6 Å resolution revealed that the intersubunit salt bridge Arg80-Asp93 contributes to the thermal stability of the hexamer (Tm = 76°C). On mutating Asp93 to Asn to break the salt bridge, the thermal stability dramatically decreased by 27.6°C. Here, on mutating Arg80 to Asn, the thermal stability also significantly decreased by 8.0°C. In the X-ray structure of the R80N mutant solved at 1.9 Å resolution the salt bridge was replaced by intersubunit hydrogen bonds that contribute to the thermal stability of the hexamer. A citrate anion from the crystallization buffer was bound at the bottom of the nucleotide-binding site via electrostatic and hydrogen-bonding interactions with six conserved residues involved in nucleotide binding. Structural analysis shows that the citrate is present at the location of the nucleotide phosphate groups.


    Related Citations: 
    • X-Ray Structure of Mycobacterium Tuberculosis Nucleoside Diphosphate Kinase.
      Chen, Y.,Morera, S.,Mocan, J.,Lascu, I.,Janin, J.
      (2002) Proteins 47: 556
    • Intersubunit Ionic Interactions Stabilize the Nucleoside Diphosphate Kinase of Mycobacterium Tuberculosis.
      Georgescauld, F.,Moynie, L.,Habersetzer, J.,Cervoni, L.,Mocan, I.,Borza, T.,Harris, P.,Dautant, A.,Lascu, I.
      (2013) Plos One 8: 57867


    Organizational Affiliation

    Institut de Biochimie et de Génétique Cellulaires, UMR 5095, CNRS, 1 Rue Camille Saint-Saëns, 33077 Bordeaux, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE KINASE
A, B, C, D, E, F
136Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)Mutation(s): 1 
Gene Names: ndkA (ndk)
EC: 2.7.4.6
Find proteins for P9WJH7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Go to UniProtKB:  P9WJH7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download SDF File 
Download CCD File 
A, D, F
CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.184 
  • Space Group: I 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.820α = 90.00
b = 113.340β = 106.40
c = 107.561γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-13
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references
  • Version 1.2: 2014-01-15
    Type: Database references
  • Version 1.3: 2014-01-22
    Type: Database references