1TPC

OFFSET OF A CATALYTIC LESION BY A BOUND WATER SOLUBLE


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

The structural basis for pseudoreversion of the E165D lesion by the secondary S96P mutation in triosephosphate isomerase depends on the positions of active site water molecules.

Komives, E.A.Lougheed, J.C.Liu, K.Sugio, S.Zhang, Z.Petsko, G.A.Ringe, D.

(1995) Biochemistry 34: 13612-13621

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structural basis for the improvement in catalytic efficiency of the mutant E165D chicken triosephosphate isomerase by the secondary mutation, S96P, has been analyzed using a combination of X-ray crystallography and Fourier transform infrared spec ...

    The structural basis for the improvement in catalytic efficiency of the mutant E165D chicken triosephosphate isomerase by the secondary mutation, S96P, has been analyzed using a combination of X-ray crystallography and Fourier transform infrared spectroscopy. All X-ray structures were of the complex of phosphoglycolohydroxamate (PGH), an intermediate analog, with the isomerase, and each was solved to a resolution of 1.9 A. Comparison of the structure of the double mutant, E165D.S96P, with that of the single mutant, E165D, as well as with the wild-type isomerase shows only insignificant differences in the positions of the side chains in all of the mutants when compared with the wild-type isomerase, except that in both the E165D and E165D.S96P mutants, the aspartate side chain was approximately 0.7 A further away from the substrate analog than the glutamate side chain. Significant differences were observed in the crystal structure of the E165D.S96P double mutant in the positions of ordered water molecules bound at the active site. The loss of two water molecules located near the side chain at position 165 was observed in isomerases containing the S96P mutation. The resulting increase in hydrophobicity of the pocket probably causes an increase in the pKa of the catalytic base, D165, thereby improving its basicity. A new ordered water molecule was observed underneath the bound PGH in the E165D.S96P structure, which likely decreases the pKa's of the substrate protons, thereby increasing their acidity. An enzyme derived carbonyl stretch at 1746 cm-1 that is only observed in the IR spectrum of the E165D.S96P double mutant isomerase with bound substrates has been assigned to a stable ground state protonated D165-enediol(ate) intermediate complex. Thus, the gain in activity resulting from the S96P second site change probably results from a combination of improving the basicity of the enzyme, improving the acidity of the substrate protons, and stabilization of a reaction intermediate. All three of these effects seem to be caused by changes in bound water molecules.


    Related Citations: 
    • S96P Change is the Second-Site Suppressor for the H95N Sluggish Mutant Isomerase
      Zhang, Z.,Sugio, S.,Komives, E.A.,Liu, K.D.,Stock, A.M.,Narayana, N.,Xuong, Ng.H.,Knowles, J.R.,Petsko, G.A.,Ringe, D.
      () TO BE PUBLISHED --: --
    • How Can a Catalytic Lesion be Offset? the Energetics of Two Pseudorevertant Triosephosphate Isomerases
      Blacklow, S.C.,Knowles, J.R.
      (1990) Biochemistry 29: 4099
    • The Structural Basis for Pseudoreversion of the E165D Lesion by the Secondary S96P Mutation in Triosephosphate Isomerase Depends on the Position of Bound Water Molecules
      Komives, E.A.,Lougheed, J.C.,Zhang, Z.,Petsko, G.A.,Ringe, D.
      () TO BE PUBLISHED --: --
    • Offset of a Catalytic Lesion (Glu165Asp) of Triosephosphate Isomerase by Bound Waters Soluble
      Zhang, Z.,Komives, E.A.,Sugio, S.,Liu, K.D.,Knowles, J.R.,Petsko, G.A.,Ringe, D.
      () TO BE PUBLISHED --: --
    • Triosephosphate Isomerase Drinks Water to Keep Healthy
      Zhang, Z.,Sugio, S.,Stock, A.M.,Komives, E.A.,Liu, K.D.,Narayana, N.,Huong, Ng.H.,Knowles, J.R.,Petsko, G.A.,Ringe, D.
      () TO BE PUBLISHED --: --


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla 92093-0601, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRIOSEPHOSPHATE ISOMERASE
1, 2
247Gallus gallusMutation(s): 0 
Gene Names: TPI1
EC: 5.3.1.1
Find proteins for P00940 (Gallus gallus)
Go to Gene View: TPI1
Go to UniProtKB:  P00940
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PGH
Query on PGH

Download SDF File 
Download CCD File 
1, 2
PHOSPHOGLYCOLOHYDROXAMIC ACID
C2 H6 N O6 P
BAXHHWZKQZIJID-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 136.400α = 90.00
b = 73.900β = 90.00
c = 55.900γ = 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: 1995-02-14
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance