1DSS

STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 

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This is version 1.2 of the entry. See complete history


Literature

Structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor.

Song, S.Y.Xu, Y.B.Lin, Z.J.Tsou, C.L.

(1999) J Mol Biol 287: 719-725

  • DOI: 10.1006/jmbi.1999.2628
  • Primary Citation of Related Structures:  
    1DSS

  • PubMed Abstract: 
  • The structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was determined in the presence of coenzyme NAD+ at 1.88 A resolution with a final R-factor of 0.175. The structure refinement was carried out on the basis of the structure of holo-GAPDH at 2 ...

    The structure of active site carboxymethylated D-glyceraldehyde-3-phosphate dehydrogenase from Palinurus versicolor was determined in the presence of coenzyme NAD+ at 1.88 A resolution with a final R-factor of 0.175. The structure refinement was carried out on the basis of the structure of holo-GAPDH at 2.0 A resolution using the program XPLOR. The carboxymethyl group connected to Cys149 is stabilized by a hydrogen bond between its OZ1 and Cys149N, and charge interaction between the carboxyl group and the nicotinamide moiety. The modification of Cys149 induced conformational changes in the active site, in particular, the site of sulphate ion 501 (the proposed attacking inorganic phosphate ion in catalysis), and segment 208-218 nearby. Extensive hydrogen-bonding interactions occur in the active site, which contribute to the higher stability of the modified enzyme. The modification of the active site did not affect the conformation of GAPDH elsewhere, including the subunit interfaces. The structures of the green and red subunits in the asymmetric unit are nearly identical, suggesting that the half-site reactivity of this enzyme is from ligand-induced rather than pre-existing asymmetry. It is proposed that the carboxymethyl group takes the place of the acyl group of the reaction intermediate, and the catalytic mechanism of this enzyme is discussed in the light of a comparison of the structures of the native and the carboxymethylated GAPDH.


    Related Citations: 
    • Structure of D-Glyceraldehyde-3-Phosphate Dehydrogenase from Palinurus Versicolor Carrying the Fluorescent Nad Derivatives at 2.7 A Resolution
      Lin, Z.J., Li, J., Zhang, F.M., Song, S.Y., Yang, J., Liang, S.J., Tsou, C.L.
      (1993) Arch Biochem Biophys 302: 161
    • Preliminary Crystallographic Studies of Lobster D-Glyceraldehyde-3-Phosphate Dehydrogenase and the Modified Enzyme Carrying the Fluorescent Derivative
      Song, S.Y., Gao, Y.G., Zhou, J.M., Tsou, C.L.
      (1983) J Mol Biol 171: 225

    Organizational Affiliation

    Institute of Biophysics, Academia Sinica, Beijing, 100101, China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASEA [auth G], B [auth R]333Panulirus versicolorMutation(s): 0 
EC: 1.2.1.12
UniProt
Find proteins for P56649 (Panulirus versicolor)
Explore P56649 
Go to UniProtKB:  P56649
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
A [auth G], B [auth R]L-PEPTIDE LINKINGC5 H9 N O4 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.1α = 90
b = 99.61β = 114.4
c = 80.69γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
WEISdata scaling
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 1997-06-04 
  • Released Date: 1998-12-09 
  • Deposition Author(s): Song, S., Lin, Z.

Revision History  (Full details and data files)

  • Version 1.0: 1998-12-09
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance