1NSQ

MECHANISM OF PHOSPHATE TRANSFER BY NUCLEOSIDE DIPHOSPHATE KINASE: X-RAY STRUCTURES OF A PHOSPHO-HISTIDINE INTERMEDIATE OF THE ENZYMES FROM DROSOPHILA AND DICTYOSTELIUM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Mechanism of phosphate transfer by nucleoside diphosphate kinase: X-ray structures of the phosphohistidine intermediate of the enzymes from Drosophila and Dictyostelium.

Morera, S.Chiadmi, M.LeBras, G.Lascu, I.Janin, J.

(1995) Biochemistry 34: 11062-11070

  • Primary Citation of Related Structures:  1NSP

  • PubMed Abstract: 
  • Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with a phosphohistidine intermediate. Crystals of the enzymes from Dictyostelium discoideum and from Drosophila melanogaster were treated with phosphoramidate, and their X-ray struc ...

    Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with a phosphohistidine intermediate. Crystals of the enzymes from Dictyostelium discoideum and from Drosophila melanogaster were treated with phosphoramidate, and their X-ray structures were determined at 2.1 and 2.2 A resolution, respectively. The atomic models, refined to R factors below 20%, show no conformation change relative to the free proteins. In both enzymes, the active site histidine was phosphorylated on N delta, and it was the only site of phosphorylation. The phosphate group interacts with the hydroxyl group of Tyr56 and with protein-bound water molecules. Its environment is compared with that of phosphohistidines in succinyl-CoA synthetase and in phosphocarrier proteins. The X-ray structures of phosphorylated NDP kinase and of previously determined complexes with nucleoside diphosphates provide a basis for modeling the Michaelis complex with a nucleoside triphosphate, that of the phosphorylated protein with a nucleoside diphosphate, and the transition state of the phosphate transfer reaction in which the gamma-phosphate is pentacoordinated.


    Related Citations: 
    • 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
    • Crystal Structure of the Awd Nucleoside Diphosphate Kinase from Drosophila
      Chiadmi, M.,Morera, S.,Lascu, I.,Dumas, C.,Lebras, G.,Veron, M.,Janin, J.
      (1993) Structure 1: 283


    Organizational Affiliation

    Laboratoire de Biologie Structurale, UMR 9920 CNRS-Université Paris-Sud, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NUCLEOSIDE DIPHOSPHATE KINASE
A, B, C
153Drosophila melanogasterGene Names: awd (K-pn)
EC: 2.7.4.6
Find proteins for P08879 (Drosophila melanogaster)
Go to UniProtKB:  P08879
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
HIP
Query on HIP
A, B, C
L-PEPTIDE LINKINGC6 H11 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.18 Å
  • R-Value Work: 0.180 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 115.750α = 90.00
b = 115.750β = 90.00
c = 98.520γ = 120.00
Software Package:
Software NamePurpose
X-PLORrefinement
X-PLORmodel building
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1995-07-10
    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