7QH0

Apo structure of the Leishmania mexicana triose-phosphate isomerase (LmTIM), N11A-E65Q variant, open conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

The Role of Asn11 in Catalysis by Triosephosphate Isomerase.

Hegazy, R.Cordara, G.Wierenga, R.K.Richard, J.P.

(2023) Biochemistry 62: 1794-1806

  • DOI: https://doi.org/10.1021/acs.biochem.3c00133
  • Primary Citation of Related Structures:  
    7QH0

  • PubMed Abstract: 

    Four catalytic amino acids at triosephosphate isomerase (TIM) are highly conserved: N11, K13, H95, and E167. Asparagine 11 is the last of these to be characterized in mutagenesis studies. The ND2 side chain atom of N11 is hydrogen bonded to the O-1 hydroxyl of enzyme-bound dihydroxyacetone phosphate (DHAP), and it sits in an extended chain of hydrogen-bonded side chains that includes T75' from the second subunit. The N11A variants of wild-type TIM from Trypanosoma brucei brucei ( Tbb TIM) and Leishmania mexicana ( Lm TIM) undergo dissociation from the dimer to monomer under our assay conditions. Values of K as = 8 × 10 3 and 1 × 10 6 M -1 , respectively, were determined for the conversion of monomeric N11A Tbb TIM and Lm TIM into their homodimers. The N11A substitution at the variant of Lm TIM previously stabilized by the E65Q substitution gives the N11A/E65Q variant that is stable to dissociation under our assay conditions. The X-ray crystal structure of N11A/E65Q Lm TIM shows an active site that is essentially superimposable on that for wild-type Tbb TIM, which also has a glutamine at position 65. A comparison of the kinetic parameters for E65Q Lm TIM and N11A/E65Q Lm TIM-catalyzed reactions of ( R )-glyceraldehyde 3-phosphate (GAP) and (DHAP) shows that the N11A substitution results in a (13-14)-fold decrease in k cat / K m for substrate isomerization and a similar decrease in k cat for DHAP but only a 2-fold decrease in k cat for GAP.


  • Organizational Affiliation

    Department of Chemistry, University at Buffalo, SUNY, Buffalo, New York 14260-3000, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Triosephosphate isomerase
A, B, C, D
251Leishmania mexicana mexicanaMutation(s): 2 
EC: 5.3.1.1
UniProt
Find proteins for P48499 (Leishmania mexicana)
Explore P48499 
Go to UniProtKB:  P48499
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48499
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.815α = 83.117
b = 73.898β = 89.327
c = 81.08γ = 77.111
Software Package:
Software NamePurpose
REFMACrefinement
PHENIXrefinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Academy of FinlandFinland--

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release
  • Version 1.1: 2023-06-21
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description