5ZGA

Crystal Structure of Triosephosphate isomerase SAD deletion and N115A mutant from Opisthorchis viverrini


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report



Literature

Structural Analysis of an Epitope Candidate of Triosephosphate Isomerase in Opisthorchis viverrini.

Son, J.Kim, S.Kim, S.E.Lee, H.Lee, M.R.Hwang, K.Y.

(2018) Sci Rep 8: 15075-15075

  • DOI: 10.1038/s41598-018-33479-8
  • Primary Citation of Related Structures:  
    5ZGA, 5ZG5, 5ZG4, 5ZFX

  • PubMed Abstract: 
  • Opisthorchis viverrini, a parasitic trematode, was recategorized as a group 1 biological carcinogen because it causes opisthorchiasis, which may result in cholangiocarcinoma. A new strategy for controlling opisthorchiasis is needed because of issues ...

    Opisthorchis viverrini, a parasitic trematode, was recategorized as a group 1 biological carcinogen because it causes opisthorchiasis, which may result in cholangiocarcinoma. A new strategy for controlling opisthorchiasis is needed because of issues such as drug resistance and reinfection. Triosephosphate isomerase (TIM), a key enzyme in energy metabolism, is regarded as a potential drug target and vaccine candidate against various pathogens. Here, we determined the crystal structures of wild-type and 3 variants of TIMs from O. viverrini (OvTIM) at high resolution. The unique tripeptide of parasite trematodes, the SAD motif, was located on the surface of OvTIM and contributed to forming a 3 10 -helix of the following loop in a sequence-independent manner. Through thermal stability and structural analyses of OvTIM variants, we found that the SAD motif induced local structural alterations of the surface and was involved in the overall stability of OvTIM in a complementary manner with another parasite-specific residue, N115. Comparison of the surface characteristics between OvTIM and Homo sapiens TIM (HsTIM) and structure-based epitope prediction suggested that the SAD motif functions as an epitope.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences & Biotechnology, Korea University, Seoul, 136-701, South Korea. chahong@korea.ac.kr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Triosephosphate isomeraseA, B, C, D269Opisthorchis viverriniMutation(s): 1 
Gene Names: T265_10017
EC: 5.3.1.1
Find proteins for A0A074Z863 (Opisthorchis viverrini)
Explore A0A074Z863 
Go to UniProtKB:  A0A074Z863
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.79 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.147 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.04α = 90
b = 92.555β = 109.39
c = 76.075γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release