2ZUA

Crystal structure of nucleoside diphosphate kinase from Haloarcula quadrata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases

Yamamura, A.Ichimura, T.Kamekura, M.Mizuki, T.Usami, R.Makino, T.Ohtsuka, J.Miyazono, K.Okai, M.Nagata, K.Tanokura, M.

(2009) Biophys J 96: 4692-4700

  • DOI: https://doi.org/10.1016/j.bpj.2009.03.012
  • Primary Citation of Related Structures:  
    2ZUA

  • PubMed Abstract: 

    Nucleoside diphosphate kinases from haloarchaea Haloarcula quadrata (NDK-q) and H. sinaiiensis (NDK-s) are identical except for one out of 154 residues, i.e., Arg(31) in NDK-q and Cys(31) in NDK-s. However, the salt-dependent activity profiles of NDK-q and NDK-s are quite different: the optimal NaCl concentrations of NDK-q and NDK-s are 1 M and 2 M, respectively. We analyzed the relationships of the secondary, tertiary, and quaternary structures and NDK activity of these NDKs at various salt concentrations, and revealed that 1), NDK-q is present as a hexamer under a wide range of salt concentrations (0.2-4 M NaCl), whereas NDK-s is present as a hexamer at an NaCl concentration above 2 M and as a dimer at NaCl concentrations below 1 M; 2), dimeric NDK-s has lower activity than hexameric NDK-s; and 3), dimeric NDK-s has higher helicity than hexameric NDK-s. We also determined the crystal structure of hexameric NDK-q, and revealed that Arg(31) plays an important role in stabilizing the hexamer. Thus the substitution of Arg (as in NDK-q) to Cys (as in NDK-s) at position 31 destabilizes the hexameric assembly, and causes dissociation to less active dimers at low salt concentrations.


  • Organizational Affiliation

    Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase
A, B, C, D
174Haloarcula quadrataMutation(s): 0 
Gene Names: ndk
UniProt
Find proteins for Q401C5 (Haloarcula quadrata)
Explore Q401C5 
Go to UniProtKB:  Q401C5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ401C5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.59 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.571α = 90
b = 73.571β = 90
c = 214.271γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-08-25
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Refinement description