2YPI

CRYSTALLOGRAPHIC ANALYSIS OF THE COMPLEX BETWEEN TRIOSEPHOSPHATE ISOMERASE AND 2-PHOSPHOGLYCOLATE AT 2.5-ANGSTROMS RESOLUTION. IMPLICATIONS FOR CATALYSIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.177 

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This is version 1.2 of the entry. See complete history


Literature

Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-A resolution: implications for catalysis.

Lolis, E.Petsko, G.A.

(1990) Biochemistry 29: 6619-6625

  • DOI: 10.1021/bi00480a010
  • Primary Citation of Related Structures:  
    2YPI

  • PubMed Abstract: 
  • The binding of the transition-state analogue 2-phosphoglycolate to triosephosphate isomerase from yeast has been investigated crystallographically. An atomic model of the enzyme-inhibitor complex has been refined against data to 2.5-A resolution to a final R factor of 0 ...

    The binding of the transition-state analogue 2-phosphoglycolate to triosephosphate isomerase from yeast has been investigated crystallographically. An atomic model of the enzyme-inhibitor complex has been refined against data to 2.5-A resolution to a final R factor of 0.18. The interactions between the inhibitor and enzyme have been analyzed. The inhibitor forms hydrogen bonds to the side chains of His 95 and Glu 165. The latter hydrogen bond confirms that Glu 165 is protonated upon PGA binding. The structure of the complexed enzyme has been compared to that of the unbound form of the enzyme, and conformational changes have been observed: the side chain of Glu 165 moves over 2 A and a 10-residue flexible loop moves over 7 A to close over the active site. Spectroscopic results of phosphoglycolic acid binding to triosephosphate isomerase that have been amassed over the years are also explained in structural terms. The implications for catalysis are noted.


    Related Citations: 
    • 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 (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 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, Massachusetts Institute of Technology, Cambridge 02139.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TRIOSEPHOSPHATE ISOMERASEA, B247Saccharomyces 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGA (Subject of Investigation/LOI)
Query on PGA

Download Ideal Coordinates CCD File 
C [auth A], D [auth B]2-PHOSPHOGLYCOLIC ACID
C2 H5 O6 P
ASCFNMCAHFUBCO-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PGA PDBBind:  2YPI Ki: 1.50e+4 (nM) from 1 assay(s)
Binding MOAD:  2YPI Ki: 1.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.177 
  • 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: 1991-01-15
    Type: Initial release
  • Version 1.1: 2008-03-25
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance