1IF2

X-RAY STRUCTURE OF LEISHMANIA MEXICANA TRIOSEPHOSPHATE ISOMERASE COMPLEXED WITH IPP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.136 

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This is version 1.2 of the entry. See complete history


Literature

Structural determinants for ligand binding and catalysis of triosephosphate isomerase.

Kursula, I.Partanen, S.Lambeir, A.M.Antonov, D.M.Augustyns, K.Wierenga, R.K.

(2001) Eur J Biochem 268: 5189-5196

  • DOI: 10.1046/j.0014-2956.2001.02452.x
  • Primary Citation of Related Structures:  
    1IF2

  • PubMed Abstract: 
  • The crystal structure of leishmania triosephosphate isomerase (TIM) complexed with 2-(N-formyl-N-hydroxy)-aminoethyl phosphonate (IPP) highlights the importance of Asn11 for binding and catalysis. IPP is an analogue of the substrate D-glyceraldehyde-3-phosphate, and it is observed to bind with its aldehyde oxygen in an oxyanion hole formed by ND2 of Asn11 and NE2 of His95 ...

    The crystal structure of leishmania triosephosphate isomerase (TIM) complexed with 2-(N-formyl-N-hydroxy)-aminoethyl phosphonate (IPP) highlights the importance of Asn11 for binding and catalysis. IPP is an analogue of the substrate D-glyceraldehyde-3-phosphate, and it is observed to bind with its aldehyde oxygen in an oxyanion hole formed by ND2 of Asn11 and NE2 of His95. Comparison of the mode of binding of IPP and the transition state analogue phosphoglycolohydroxamate (PGH) suggests that the Glu167 side chain, as well as the triose part of the substrate, adopt different conformations as the catalysed reaction proceeds. Comparison of the TIM-IPP and the TIM-PGH structures with other liganded and unliganded structures also highlights the conformational flexibility of the ligand and the active site, as well as the conserved mode of ligand binding.


    Organizational Affiliation

    Biocenter Oulu and Department of Biochemistry, University of Oulu, FIN-90014, Oulu, Finland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRIOSEPHOSPHATE ISOMERASEA251Leishmania mexicanaMutation(s): 1 
EC: 5.3.1.1
UniProt
Find proteins for P48499 (Leishmania mexicana)
Explore P48499 
Go to UniProtKB:  P48499
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
129 (Subject of Investigation/LOI)
Query on 129

Download Ideal Coordinates CCD File 
B [auth A][2(FORMYL-HYDROXY-AMINO)-ETHYL]-PHOSPHONIC ACID
C3 H8 N O5 P
NBAIGNUEKZLOMI-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.136 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.234α = 90
b = 52.825β = 118.03
c = 58.937γ = 90
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4data 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: 2001-08-17
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance