2HUR

Escherichia coli nucleoside diphosphate kinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure of the Escherichia coli nucleoside diphosphate kinase reveals a new quaternary architecture for this enzyme family

Moynie, L.Giraud, M.-F.Georgescauld, F.Lascu, I.Dautant, A.

(2007) Proteins 67: 755-765

  • DOI: 10.1002/prot.21316
  • Also Cited By: 3ZTS, 3ZTR, 3ZTQ, 3ZTP, 3ZTO

  • PubMed Abstract: 
  • Nucleoside diphosphate kinase (NDPK) catalyzes the transfer of gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. The subunit folding and the dimeric basic structural unit are remarkably the same for available structures but, d ...

    Nucleoside diphosphate kinase (NDPK) catalyzes the transfer of gamma-phosphate from nucleoside triphosphates to nucleoside diphosphates. The subunit folding and the dimeric basic structural unit are remarkably the same for available structures but, depending on species, dimers self-associate to form hexamers or tetramers. The crystal structure of the Escherichia coli NDPK reveals a new tetrameric quaternary structure for this protein family. The two tetramers differ by the relative orientation of interacting dimers, which face either the convex or the concave side of their central sheet as in either Myxococcus xanthus (type I) or E. coli (type II), respectively. In the type II tetramer, the subunits interact by a new interface harboring a zone called the Kpn loop as in hexamers, but by the opposite face of this loop. The evolutionary conservation of the interface residues indicates that this new quaternary structure seems to be the most frequent assembly mode in bacterial tetrameric NDP kinases.


    Related Citations: 
    • Crystal structure of Myxococcus xanthus nucleoside diphosphate kinase and its interaction with a nucleotide substrate at 2.0 A resolution
      Williams, R.L.,Oren, D.A.,Inouye, S.,Inouye, M.,Arnold, E.
      (1993) J.Mol.Biol. 234: 1230
    • Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8 A resolution.
      LeBras, G.,Lascu, I.,Lacombe, M.L.,Janin, J.
      (1994) J.Mol.Biol. 243: 873
    • Nucleoside diphosphate kinase from Escherichia coli
      Almaula, N.,Lu, Q.,Delgado, J.,Belkin, S.,Inouye, M.
      (1995) J.Bacteriol. 177: 2524


    Organizational Affiliation

    Institut de Biochimie et Génétique Cellulaires, UMR 5095 CNRS-Université Victor Segalen Bordeaux 2, 33077 Bordeaux cedex, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE KINASE
A, B, C, D, E, F
142Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ndk
EC: 2.7.4.6
Find proteins for P0A763 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A763
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 118.904α = 90.00
b = 76.095β = 112.99
c = 104.588γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
CCP4data scaling
MOSFLMdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-04-10
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance