5IOL

Crystal structure of Nucleoside Diphosphate Kinase from Schistosoma mansoni


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

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This is version 1.4 of the entry. See complete history


Literature

Characterization of a Schistosoma mansoni NDPK expressed in sexual and digestive organs.

Torini, J.R.de Freitas Fernandes, A.Balasco Serrao, V.H.Romanello, L.Bird, L.E.Nettleship, J.E.Owens, R.J.Brandao-Neto, J.Zeraik, A.E.DeMarco, R.D'Muniz Pereira, H.

(2019) Mol Biochem Parasitol : 111187-111187

  • DOI: https://doi.org/10.1016/j.molbiopara.2019.111187
  • Primary Citation of Related Structures:  
    5IOL, 5IOM, 5KK8

  • PubMed Abstract: 

    Nucleoside diphosphate kinases (NDPKs) are crucial to keep the high triphosphate nucleotide levels in the biological process. The enzymatic mechanism has been extensively described; however, the structural characteristics and kinetic parameters have never been fully determined. In Schistosoma mansoni, NDPK (SmNDPK) is directly involved in the pyrimidine and purine salvage pathways, being essential for nucleotide metabolism. The SmNDPK enzymatic activity is the highest of the known purine metabolisms when compared to the mammalian NDPKs, suggesting the importance of this enzyme in the worm metabolism. Here, we report the recombinant expression of SmNDPK that resulted in 1.7 and 1.9 Å apo-form structure in different space-groups, as well as the 2.1 Å SmNDPK.ADP complex. The binding and kinetic assays reveal the ATP-dependence for enzyme activation. Moreover, in situ hybridization showed that SmNDPK transcripts are found in reproductive organs and in the esophagus gland of adult worms, which can be intrinsically related with the oviposition and digestive processes. These results will help us fully understand the crucial participation of this enzyme in Schistosoma mansoni and its importance for the pathology of the disease.


  • Organizational Affiliation

    Laboratório de Biologia Estrutural, Instituto de Física de São Carlos, Universidade de São Paulo, 13563-120, São Carlos, SP, Brazil.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nucleoside diphosphate kinase
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
150Schistosoma mansoniMutation(s): 0 
Gene Names: Smp_092750
EC: 2.7.4.6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 211.76α = 90
b = 82.27β = 104.89
c = 122.37γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data scaling
PHASERphasing
PDB_EXTRACTdata extraction
xia2data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2012/14223-9
Brazilian National Council for Scientific and Technological Development (CNPq)Brazil474402/2013-4

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-08
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description