2X1S

Crystallographic binding studies with an engineered monomeric variant of triosephosphate isomerase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystallographic Binding Studies with an Engineered Monomeric Variant of Triosephosphate Isomerase

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

(2010) Acta Crystallogr.,Sect.D 66: 934

  • DOI: 10.1107/S0907444910025710
  • Primary Citation of Related Structures:  

  • 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 ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE, GLYCOSOMAL
A, B
238Trypanosoma brucei bruceiMutation(s): 12 
EC: 5.3.1.1
Find proteins for P04789 (Trypanosoma brucei brucei)
Go to UniProtKB:  P04789
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
X1S
Query on X1S

Download SDF File 
Download CCD File 
A, B
3-SULFOPROPANOIC ACID
C3 H6 O5 S
OURSFPZPOXNNKX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.93 Å
  • R-Value Free: 0.201 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 45.820α = 90.00
b = 86.170β = 98.30
c = 56.280γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOLREPphasing
XSCALEdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2012-04-11
    Type: Atomic model, Database references, Refinement description, Version format compliance
  • Version 1.2: 2017-06-28
    Type: Data collection