1GD1

STRUCTURE OF HOLO-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus at 1.8 A resolution.

Skarzynski, T.Moody, P.C.Wonacott, A.J.

(1987) J Mol Biol 193: 171-187

  • DOI: 10.1016/0022-2836(87)90635-8
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus has been crystallographically refined at 1.8 A resolution using restrained least-squares refinement methods. The final crystallographic R-factor for 93,12 ...

    The structure of holo-glyceraldehyde-3-phosphate dehydrogenase from Bacillus stearothermophilus has been crystallographically refined at 1.8 A resolution using restrained least-squares refinement methods. The final crystallographic R-factor for 93,120 reflexions with F greater than 3 sigma (F) is 0.177. The asymmetric unit of the crystal contains a complete tetramer, the final model of which incorporates a total of 10,272 unique protein and coenzyme atoms together with 677 bound solvent molecules. The structure has been analysed with respect to molecular symmetry, intersubunit contacts, coenzyme binding and active site geometry. The refined model shows the four independent subunits to be remarkable similar apart from local deviations due to intermolecular contacts within the crystal lattice. A number of features are revealed that had previously been misinterpreted from an earlier 2.7 A electron density map. Arginine at position 195 (previously thought to be a glycine) contributes to the formation of the anion binding sites in the active site pocket, which are involved in binding of the substrate and inorganic phosphates during catalysis. This residue seems to be structurally equivalent to the conserved Arg194 in the enzyme from other sources. In the crystal both of the anion binding sites are occupied by sulphate ions. The ND atom of the catalytically important His176 is hydrogen-bonded to the main-chain carbonyl oxygen of Ser177, thus fixing the plane of the histidine imidazole ring and preventing rotation. The analysis has revealed the presence of several internal salt-bridges stabilizing the tertiary and quaternary structure. A significant number of buried water molecules have been found that play an important role in the structural integrity of the molecule.


    Related Citations: 
    • 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 Escherichia Coli
      Branlant, C., Oster, T., Branlant, G.
      (1989) Gene 75: 145
    • Coenzyme-Induced Conformational Changes in Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophillus
      Skarzynski, T., Wonacott, A.J.
      (1988) J Mol Biol 203: 1097
    • 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
    • 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
      Dalziel, K., Mcferran, N.V., Wonacott, A.J.
      (1981) Philos Trans R Soc London,ser B 293: 105
    • Enzymes from Thermophilic Bacteria
      Walker, J.E.
      (1978) Proc Febs Meet 52: 211
    • 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
    • Glyceraldehyde-3-Phosphate Dehydrogenase from Bacillus Stearothermophilus
      Suzuki, K., Harris, J.I.
      (1971) FEBS Lett 13: 217

    Organizational Affiliation

    Sealy Center for Structural Biology, Department of Human Biological Chemistry and Genetics, University of Texas Medical Branch, 301 University Blvd, Galveston, TX 77555-1157, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HOLO-D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE
O, P, Q, R
334Geobacillus stearothermophilusMutation(s): 0 
Gene Names: BACILLUS STEAROTHERMOPHILUSgap
EC: 1.2.1.12
Find proteins for P00362 (Geobacillus stearothermophilus)
Go to UniProtKB:  P00362
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download CCD File 
O, P, Q, R
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
SO4
Query on SO4

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: 1.80 Å
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.44α = 90
b = 124.1β = 108.98
c = 82.54γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1988-01-16
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance