1YPI

STRUCTURE OF YEAST TRIOSEPHOSPHATE ISOMERASE AT 1.9-ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of yeast triosephosphate isomerase at 1.9-A resolution.

Lolis, E.Alber, T.Davenport, R.C.Rose, D.Hartman, F.C.Petsko, G.A.

(1990) Biochemistry 29: 6609-6618


  • PubMed Abstract: 
  • The structure of yeast triosephosphate isomerase (TIM) has been solved at 3.0-A resolution and refined at 1.9-A resolution to an R factor of 21.0%. The final model consists of all non-hydrogen atoms in the polypeptide chain and 119 water molecules, a ...

    The structure of yeast triosephosphate isomerase (TIM) has been solved at 3.0-A resolution and refined at 1.9-A resolution to an R factor of 21.0%. The final model consists of all non-hydrogen atoms in the polypeptide chain and 119 water molecules, a number of which are found in the interior of the protein. The structure of the active site clearly indicates that the carboxylate of the catalytic base, Glu 165, is involved in a hydrogen-bonding interaction with the hydroxyl of Ser 96. In addition, the interactions of the other active site residues, Lys 12 and His 95, are also discussed. For the first time in any TIM structure, the "flexible loop" has well-defined density; the conformation of the loop in this structure is stabilized by a crystal contact. Analysis of the subunit interface of this dimeric enzyme hints at the source of the specificity of one subunit for another and allows us to estimate an association constant of 10(14)-10(16) M-1 for the two monomers. The analysis also suggests that the interface may be a particularly good target for drug design. The conserved positions (20%) among sequences from 13 sources ranging on the evolutionary scale from Escherichia coli to humans reveal the intense pressure to maintain the active site structure.


    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
    • Crystallography and Site-Directed Mutagenesis of Yeast Triosephosphate Isomerase. What Can We Learn About Catalysis from a (Double Quote)Simple(Double Quote) Enzyme (Question Mark)
      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
    • 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
    • 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


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, Cambridge 02139.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE
A, B
247Saccharomyces cerevisiae (strain ATCC 204508 / S288c)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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 61.150α = 90.00
b = 98.550β = 91.20
c = 49.260γ = 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: 1991-01-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance