2GD1

COENZYME-INDUCED CONFORMATIONAL CHANGES IN GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILLUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Coenzyme-induced conformational changes in glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus.

Skarzynski, T.Wonacott, A.J.

(1988) J.Mol.Biol. 203: 1097-1118


  • PubMed Abstract: 
  • The structure of apo-glyceraldehyde-3-phosphate dehydrogenase (GAPDHase) from Bacillus stearothermophilus has been refined using a restrained least-squares method. The final crystallographic R-factor is 0.177 for all 53,315 reflections between 7.0 an ...

    The structure of apo-glyceraldehyde-3-phosphate dehydrogenase (GAPDHase) from Bacillus stearothermophilus has been refined using a restrained least-squares method. The final crystallographic R-factor is 0.177 for all 53,315 reflections between 7.0 and 2.5 A. The resulting model has been analysed with respect to lattice interactions, molecular symmetry, temperature factors and solvent structure showing that, apart from local deviations due to intermolecular contact, the molecule exhibits a very high degree of local 222 symmetry. Analysis of differences between the structure of apo-GAPDHase and the previously refined holo-GAPDHase at 1.8 A resolution reveals details of conformational change in the enzyme induced by cofactor binding. The change, which was previously described as a rigid-body rotation of the coenzyme-binding domain with respect to the catalytic domain, is of more complex nature and involves relative shifts of several structural elements in the coenzyme-binding domain and some small changes in the catalytic domain. A possible mechanism of this conformational change is proposed based on the comparison of the refined structures and model-building studies. According to this mechanism, the adenosine moiety of NAD can initially bind to the protein in the apo-enzyme conformation. Several attractive interactions resulting from the initial binding of the coenzyme trigger conformational changes in the molecule of GAPDHase that: (1) create the productive nicotinamide-moiety binding site; (2) improve enzyme-coenzyme interactions at the adenosine moiety; (3) modify the active site to optimize the positioning of catalytic residues and ion-binding sites. Implications of the proposed mechanism for existing experimental data on binding of NAD analogues to GAPDHase are discussed.


    Related Citations: 
    • Structural Evidence for Ligand-Induced Sequential Conformational Changes in Glyceraldehyde 3-Phosphate Dehydrogenase
      Leslie, A.G.W.,Wonacott, A.J.
      (1984) J.Mol.Biol. 178: 743
    • Sequence and Structure of D-Glyceraldehyde 3-Phosphate Dehydrogenase from Bacillus Stearothermophilus
      Biesecker, G.,Harris, J.I.,Thierry, J.C.,Walker, J.E.,Wonacott, A.J.
      (1977) Nature 266: 328
    • Coenzyme Binding and Co-Operativity in D-Glyceraldehyde 3-Phosphate Dehydrogenase
      Biesecker, G.,Wonacott, A.J.
      (1977) Biochem.Soc.Trans. 5: 647
    • Structure of Holo-Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus at 1.8 Angstroms Resolution
      Skarzynski, T.,Moody, P.C.E.,Wonacott, A.J.
      (1987) J.Mol.Biol. 193: 171
    • Enzymes from Thermophilic Bacteria
      Walker, J.E.
      (1978) Proc.FEBS Meet. 52: 211
    • Glyceraldehyde-3-Phosphate Dehydrogenase
      Dalziel, K.,Mcferran, N.V.,Wonacott, A.J.
      (1981) Philos.Trans.R.Soc.London,Ser.B 293: 105
    • Nucleotide Sequence Determination of the DNA Region Coding for Bacillus Stearothermophilus Glyceraldehyde-3-Phosphate Dehydrogenase and of the Flanking DNA Regions Required for its Expression in Escherichia Coli
      Branlant, C.,Oster, T.,Branlant, G.
      (1989) Gene 75: 145
    • Coenzyme Binding in Crystals of Glyceraldehyde-3-Phosphate Dehydrogenase
      Leslie, A.G.W.,Wonacott, A.J.
      (1983) J.Mol.Biol. 165: 375
    • Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus
      Suzuki, K.,Harris, J.I.
      (1971) FEBS Lett. 13: 217


    Organizational Affiliation

    Blackett Laboratory, Imperial College, London, England.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
APO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
O, P, Q, R
334Geobacillus stearothermophilusMutation(s): 0 
Gene Names: gap
EC: 1.2.1.12
Find proteins for P00362 (Geobacillus stearothermophilus)
Go to UniProtKB:  P00362
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
O, P, Q, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.800α = 90.00
b = 129.200β = 107.30
c = 83.100γ = 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: 1989-10-15
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance