1KV5

Structure of Trypanosoma brucei brucei TIM with the salt-bridge-forming residue Arg191 mutated to Ser

• PDB DOI: https://doi.org/10.2210/pdb1KV5/pdb

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


• Deposited: 2002-01-25 Released: 2002-03-29 
• Deposition Author(s): Kursula, I., Partanen, S., Lambeir, A.-M., Wierenga, R.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.175 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 

Starting Model: experimental

Literature

The importance of the conserved Arg191-Asp227 salt bridge of triosephosphate isomerase for folding, stability, and catalysis

Kursula, I., Partanen, S., Lambeir, A.-M., Wierenga, R.K.

(2002) FEBS Lett 518: 39-42

• PubMed: 11997014 
• DOI: https://doi.org/10.1016/s0014-5793(02)02639-x
• Primary Citation of Related Structures:  
  1KV5


• PubMed Abstract: 
  

  Triosephosphate isomerase (TIM) has a conserved salt bridge 20 A away from both the active site and the dimer interface. In this study, four salt bridge mutants of Trypanosoma brucei brucei TIM were characterized. The folding and stability of the mutants are impaired compared to the wild-type enzyme. This salt bridge is part of a hydrogen bonding network which tethers the C-terminal beta7alpha7beta8alpha8 unit to the bulk of the protein. In the variants D227N, D227A, and R191S, this network is preserved, as can be deduced from the structure of the R191S variant. In the R191A variant, the side chain at position 191 cannot contribute to this network. Also the catalytic power of this variant is most affected.

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Organizational Affiliation: 

Department of Biochemistry and Biocenter Oulu, University of Oulu, P.O. Box 3000, FIN-90014 Oulu, Finland.

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)

Macromolecule Content

• Total Structure Weight: 54.52 kDa 
• Atom Count: 4,682 
• Modelled Residue Count: 498 
• Deposited Residue Count: 500 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
triosephosphate isomerase, glycosomal	A, B	250	Trypanosoma brucei brucei	Mutation(s): 1  EC: 5.3.1.1
UniProt
Find proteins for P04789 (Trypanosoma brucei brucei) Go to UniProtKB:  P04789

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGA	C [auth A], G [auth B]	2-PHOSPHOGLYCOLIC ACID C2 H5 O6 P ASCFNMCAHFUBCO-UHFFFAOYSA-N
DTT	D [auth A]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C4 H10 O2 S2 VHJLVAABSRFDPM-IMJSIDKUSA-N
SO4	H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], F [auth A], I [auth B], J [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
PGA	PDBBind:  1KV5	Ki: 6.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.175 
• R-Value Work: 0.143 
• R-Value Observed: 0.145 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.943	α = 90
b = 100.638	β = 90
c = 109.35	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-03-29 
Deposition Author(s): Kursula, I., Partanen, S., Lambeir, A.-M., Wierenga, R.K.

Revision History  

• Version 1.0: 2002-03-29
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2021-10-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2023-08-16
  Changes: Data collection, Refinement description