3YPI

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Observed: 0.184 

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

  • DOI: https://doi.org/10.1021/bi00226a005
  • Primary Citation of Related Structures:  
    3YPI

  • 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 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 ...

    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: 
    • 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
    • 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 Harb Symp Quant Biol 52: 603
    • 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
    • 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRIOSEPHOSPHATE ISOMERASE
A, B
247Saccharomyces cerevisiaeMutation(s): 0 
EC: 5.3.1.1
UniProt
Find proteins for P00942 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00942 
Go to UniProtKB:  P00942
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00942
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGH
Query on PGH

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
PHOSPHOGLYCOLOHYDROXAMIC ACID
C2 H6 N O6 P
BAXHHWZKQZIJID-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Observed: 0.184 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.35α = 90
b = 83.97β = 99.7
c = 38.67γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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