1NCL

THERMAL STABILITY OF HEXAMERIC AND TETRAMERIC NUCLEOSIDE, DIPHOSPHATE KINASES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Thermal stability of hexameric and tetrameric nucleoside diphosphate kinases. Effect of subunit interaction.

Giartosio, A.Erent, M.Cervoni, L.Morera, S.Janin, J.Konrad, M.Lascu, I.

(1996) J.Biol.Chem. 271: 17845-17851


  • PubMed Abstract: 
  • The eukaryotic nucleoside diphosphate (NDP) kinases are hexamers, while the bacterial NDP kinases are tetramers made of small, single domain subunits. These enzymes represent an ideal model for studying the effect of subunit interaction on protein st ...

    The eukaryotic nucleoside diphosphate (NDP) kinases are hexamers, while the bacterial NDP kinases are tetramers made of small, single domain subunits. These enzymes represent an ideal model for studying the effect of subunit interaction on protein stability. The thermostability of NDP kinases of each class was studied by differential scanning calorimetry and biochemical methods. The hexameric NDP kinase from Dictyostelium discoideum displays one single, irreversible differential scanning calorimetry peak (Tm 62 degrees C) over a broad protein concentration, indicating a single step denaturation. The thermal stability of the protein was increased by ADP. The P105G substitution, which affects a loop implicated in subunit contacts, yields a protein that reversibly dissociates to folded monomers at 38 degrees C before the irreversible denaturation occurs (Tm 47 degrees C). ADP delays the dissociation, but does not change the Tm. These data indicate a "coupling" of the quaternary structure with the tertiary structure in the wild-type, but not in the mutated protein. We describe the x-ray structure of the P105G mutant at 2.2-A resolution. It is very similar to that of the wild-type protein. Therefore, a minimal change in the structure leads to a dramatic change of protein thermostability. The NDP kinase from Escherichia coli behaves like the P105G mutant of the Dictyostelium NDP kinase. The detailed study of their thermostability is important, since biological effects of thermolabile NDP kinases have been described in several organisms.


    Related Citations: 
    • Refined X-Ray Structure of Dictyostelium Discoideum Nucleoside Diphosphate Kinase at 1.8 A Resolution
      Morera, S.,Lebras, G.,Lascu, I.,Lacombe, M.L.,Veron, M.,Janin, J.
      (1994) J.Mol.Biol. 243: 873
    • X-Ray Structure of Nucleoside Diphosphate Kinase
      Dumas, C.,Lascu, I.,Morera, S.,Glaser, P.,Fourme, R.,Wallet, V.,Lacombe, M.L.,Veron, M.,Janin, J.
      (1992) Embo J. 11: 3203


    Organizational Affiliation

    Dipartimento di Scienze Biochimiche "A. Rossi Fanelli" and Center of Molecular Biology of C.N.R., Università degli Studi "La Sapienza, " 00185 Roma, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE KINASE
A
150Dictyostelium discoideumMutation(s): 1 
Gene Names: ndkC-1, ndkC-2 (gip17, ndkB, gip17, ndkB)
EC: 2.7.4.6
Find proteins for P22887 (Dictyostelium discoideum)
Go to UniProtKB:  P22887
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.181 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 74.300α = 90.00
b = 74.300β = 90.00
c = 105.300γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
MOSFLMdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-11-08
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance