Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase

Experimental Data Snapshot

  • Resolution: 1.98 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

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Crystallographic Binding Studies with an Engineered Monomeric Variant of Triosephosphate Isomerase

Salin, M.Kapetaniou, E.G.Vaismaa, M.Lajunen, M.Casteleijn, M.G.Neubauer, P.Salmon, L.Wierenga, R.

(2010) Acta Crystallogr D Biol Crystallogr 66: 934

  • DOI: https://doi.org/10.1107/S0907444910025710
  • Primary Citation of Related Structures:  
    2X16, 2X1R, 2X1S, 2X1T, 2X1U, 2X2G

  • PubMed Abstract: 

    Crystallographic binding studies have been carried out to probe the active-site binding properties of a monomeric variant (A-TIM) of triosephosphate isomerase (TIM). These binding studies are part of a structure-based directed-evolution project aimed towards changing the substrate specificity of monomeric TIM and are therefore aimed at finding binders which are substrate-like molecules. A-TIM has a modified more extended binding pocket between loop-7 and loop-8 compared with wild-type TIM. The A-TIM crystals were grown in the presence of citrate, which is bound in the active site of each of the two molecules in the asymmetric unit. In this complex, the active-site loops loop-6 and loop-7 adopt the closed conformation, similar to that observed in liganded wild-type TIM. Extensive crystal-soaking protocols have been developed to flush the bound citrate out of the active-site pocket of both molecules and the crystal structure shows that the unliganded open conformation of the A-TIM active site is the same as in unliganded wild-type TIM. It is also shown that sulfonate compounds corresponding to the transition-state analogue 2-phosphoglycolate bind in the active site, which has a closed conformation. It is also shown that the new binding pocket of A-TIM can bind 3-phosphoglycerate (3PGA; an analogue of a C4-sugar phosphate) and 4-phospho-D-erythronohydroxamic acid (4PEH; an analogue of a C5-sugar phosphate). Therefore, these studies have provided a rationale for starting directed-evolution experiments aimed at generating the catalytic properties of a C5-sugar phosphate isomerase on the A-TIM framework.

  • Organizational Affiliation

    Department of Biochemistry, PO Box 3000, 90014 University of Oulu, Finland.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
238Trypanosoma brucei bruceiMutation(s): 12 
Find proteins for P04789 (Trypanosoma brucei brucei)
Explore P04789 
Go to UniProtKB:  P04789
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04789
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.98 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.94α = 90
b = 86.92β = 98.58
c = 56.28γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2012-04-11
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Refinement description, Version format compliance
  • Version 1.2: 2019-07-24
    Changes: Data collection
  • Version 1.3: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description