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 

wwPDB Validation 3D Report Full Report


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

  • 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 carr ...

    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: 
    • 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
    • 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


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
D-GLYCERALDEHYDE-3-PHOSPHATE-DEHYDROGENASE
G, R
333Panulirus versicolorEC: 1.2.1.12
Find proteins for P56649 (Panulirus versicolor)
Go to UniProtKB:  P56649
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
G, R
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
NAD
Query on NAD

Download SDF File 
Download CCD File 
G, R
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CCS
Query on CCS
G, 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 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.100α = 90.00
b = 99.610β = 114.40
c = 80.690γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
WEISdata scaling
WEISdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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