Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 59.90 kDa 
• Atom Count: 4491 
• Residue Count: 496 
• Unique protein chains: 1

5ZG5

Crystal Structure of Triosephosphate isomerase SADsubAAA mutant from Opisthorchis viverrini

• DOI: 10.2210/pdb5ZG5/pdb

• Classification: ISOMERASE
• Organism(s): Opisthorchis viverrini
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2018-03-07 Released: 2018-10-24 
• Deposition Author(s): Son, J., Kim, S., Kim, S.E., Lee, H., Lee, M.R., Hwang, K.Y.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 

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

• PubMed: 30305716 
• 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 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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B	272	Opisthorchis viverrini	Mutation(s): 2  Gene Names: T265_10017 EC: 5.3.1.1
Find proteins for A0A074Z863 (Opisthorchis viverrini) Explore A0A074Z863  Go to UniProtKB:  A0A074Z863

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.195 
• R-Value Work: 0.171 
• R-Value Observed: 0.171 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.84	α = 90
b = 90.369	β = 90
c = 102.265	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2018-03-07 
• Released Date: 2018-10-24 
Deposition Author(s): Son, J., Kim, S., Kim, S.E., Lee, H., Lee, M.R., Hwang, K.Y.

Revision History 

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