2I9E

Structure of Triosephosphate Isomerase of Tenebrio molitor

• PDB DOI: https://doi.org/10.2210/pdb2I9E/pdb

• Classification: ISOMERASE
• Organism(s): Tenebrio molitor
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-05 Released: 2006-09-26 
• Deposition Author(s): Schmidt, A., Scheerer, P., Wessner, H., Hoehne, W., Krauss, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 

Starting Model: experimental

Literature

A coleopteran triosephosphate isomerase: X-ray structure and phylogenetic impact of insect sequences.

Knobeloch, D., Schmidt, A., Scheerer, P., Krauss, N., Wessner, H., Scholz, C., Kuttner, G., von Rintelen, T., Wessel, A., Hohne, W.

(2010) Insect Mol Biol 19: 35-48

• PubMed: 19849721 
• DOI: https://doi.org/10.1111/j.1365-2583.2009.00928.x
• Primary Citation of Related Structures:  
  2I9E


• PubMed Abstract: 
  

  A coleopteran triosephosphate isomerase (TIM) from Tenebrio molitor (yellow mealworm beetle) was recombinantly expressed in Escherichia coli and characterized with respect to thermal stability, kinetic parameters and oligomeric state. The enzyme was successfully crystallized and the structure determined by X-ray analysis to 2.0 A resolution. This is the first example of an invertebrate TIM. We compare structural features with known structures of TIMs from microorganisms, plants and vertebrates, and discuss the utility of the Tenebrio TIM sequence, together with several newly sequenced insect TIMs, for molecular phylogenetic analysis.

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Organizational Affiliation: 

Institut für Biochemie, Charité- Universitätsmedizin Berlin, Berlin.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 113.38 kDa 
• Atom Count: 7,898 
• Modelled Residue Count: 988 
• Deposited Residue Count: 1,036 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Triosephosphate isomerase	A, B, C, D	259	Tenebrio molitor	Mutation(s): 3  Gene Names: tpi EC: 5.3.1.1
UniProt
Find proteins for Q8MPF2 (Tenebrio molitor) Explore Q8MPF2  Go to UniProtKB:  Q8MPF2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	E [auth B], F [auth B], G [auth C], H [auth D], I [auth D]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.239 
• R-Value Work: 0.219 
• R-Value Observed: 0.221 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.06	α = 90
b = 145.08	β = 95.61
c = 94.28	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-26 
Deposition Author(s): Schmidt, A., Scheerer, P., Wessner, H., Hoehne, W., Krauss, N.

Revision History  

• Version 1.0: 2006-09-26
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-04-15
  Changes: Database references
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2023-08-30
  Changes: Data collection, Refinement description