3YPI

ELECTROPHILIC CATALYSIS IN TRIOSEPHOSPHASE ISOMERASE: THE ROLE OF HISTIDINE-95


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Electrophilic catalysis in triosephosphate isomerase: the role of histidine-95.

Komives, E.A.Chang, L.C.Lolis, E.Tilton, R.F.Petsko, G.A.Knowles, J.R.

(1991) Biochemistry 30: 3011-3019


  • PubMed Abstract: 
  • Electrophilic catalysis by histidine-95 in triosephosphate isomerase has been probed by using Fourier transform infrared spectroscopy and X-ray crystallography. The carbonyl stretching frequency of dihydroxyacetone phosphate bound to the wild-type en ...

    Electrophilic catalysis by histidine-95 in triosephosphate isomerase has been probed by using Fourier transform infrared spectroscopy and X-ray crystallography. The carbonyl stretching frequency of dihydroxyacetone phosphate bound to the wild-type enzyme is known to be 19 cm-1 lower (at 1713 cm-1) than that of dihydroxyacetone phosphate free in solution (at 1732 cm-1), and this decrease in stretching frequency has been ascribed to an enzymic electrophile that polarizes the substrate carbonyl group toward the transition state for the enolization. Infrared spectra of substrate bound to two site-directed mutants of yeast triosephosphate isomerase in which histidine-95 has been changed to glutamine or to asparagine show unperturbed carbonyl stretching frequencies between 1732 and 1742 cm-1. The lack of carbonyl polarization when histidine-95 is removed suggests that histidine-95 is indeed the catalytic electrophile, at least for dihydroxyacetone phosphate. Kinetic studies of the glutamine mutant (H95Q) have shown that the enzyme follows a subtly different mechanism of proton transfers involving only a single acid-base catalytic group. These findings suggest an additional role for histidine-95 as a general acid-base catalyst in the wild-type enzyme. The X-ray crystal structure of the H95Q mutant with an intermediate analogue, phosphoglycolohydroxamate, bound at the active site has been solved to 2.8-A resolution, and this structure clearly implicates glutamate-165, the catalytic base in the wild-type isomerase, as the sole acid-base catalyst for the mutant enzyme.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Crystallization of Yeast Triose Phosphate Isomerase from Polyethylene Glycol. Protein Crystal Formation Following Phase Separation
      Alber, T.,Hartman, F.C.,Johnson, R.M.,Petsko, G.A.,Tsernoglou, D.
      (1981) J.Biol.Chem. 256: 1356
    • Structure of Yeast Triosephosphate Isomerase at 1.9-Angstroms Resolution
      Lolis, E.,Alber, T.,Davenport, R.C.,Rose, D.,Hartman, F.C.,Petsko, G.A.
      (1990) Biochemistry 29: 6609
    • Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a "Simple" Enzyme?
      Alber, T.C.,Davenportjunior, R.C.,Giammona, D.A.,Lolis, E.,Petsko, G.A.,Ringe, D.
      (1987) Cold Spring Harbor Symp.Quant.Biol. 52: 603
    • Crystallographic Analysis of the Complex between Triosephosphate Isomerase and 2-Phosphoglycolate at 2.5-Angstroms Resolution. Implications for Catalysis
      Lolis, E.,Petsko, G.A.
      (1990) Biochemistry 29: 6619
    • On the Three-Dimensional Structure and Catalytic Mechanism of Triose Phosphate Isomerase
      Alber, T.,Banner, D.W.,Bloomer, A.C.,Petsko, G.A.,Phillips, D.,Rivers, P.S.,Wilson, I.A.
      (1981) Philos.Trans.R.Soc.London,Ser.B 293: 159


    Organizational Affiliation

    Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE
A, B
247Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TPI1
EC: 5.3.1.1
Find proteins for P00942 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: TPI1
Go to UniProtKB:  P00942
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGH
Query on PGH

Download SDF File 
Download CCD File 
A, B
PHOSPHOGLYCOLOHYDROXAMIC ACID
C2 H6 N O6 P
BAXHHWZKQZIJID-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 74.350α = 90.00
b = 83.970β = 99.70
c = 38.670γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-04-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance