3CMC

Thioacylenzyme intermediate of Bacillus stearothermophilus phosphorylating GAPDH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Trapping of the Thioacylglyceraldehyde-3-phosphate Dehydrogenase Intermediate from Bacillus stearothermophilus: DIRECT EVIDENCE FOR A FLIP-FLOP MECHANISM

Moniot, S.Bruno, S.Vonrhein, C.Didierjean, C.Boschi-Muller, S.Vas, M.Bricogne, G.Branlant, G.Mozzarelli, A.Corbier, C.

(2008) J Biol Chem 283: 21693-21702

  • DOI: 10.1074/jbc.M802286200
  • Primary Citation of Related Structures:  
    3CMC

  • PubMed Abstract: 
  • The crystal structure of the thioacylenzyme intermediate of the phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus stearothermophilus has been solved at 1.8A resolution. Formation of the intermediate was obtained by diffusion of the natural substrate within the crystal of the holoenzyme in the absence of inorganic phosphate ...

    The crystal structure of the thioacylenzyme intermediate of the phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPDH) from Bacillus stearothermophilus has been solved at 1.8A resolution. Formation of the intermediate was obtained by diffusion of the natural substrate within the crystal of the holoenzyme in the absence of inorganic phosphate. To define the soaking conditions suitable for the isolation and accumulation of the intermediate, a microspectrophotometric characterization of the reaction of GAPDH in single crystals was carried out, following NADH formation at 340 nm. When compared with the structure of the Michaelis complex (Didierjean, C., Corbier, C., Fatih, M., Favier, F., Boschi-Muller, S., Branlant, G., and Aubry, A. (2003) J. Biol. Chem. 278, 12968-12976) the 206-210 loop is shifted and now forms part of the so-called "new P(i)" site. The locations of both the O1 atom and the C3-phosphate group of the substrate are also changed. Altogether, the results provide evidence for the flipping of the C3-phosphate group occurring concomitantly or after the redox step.


    Organizational Affiliation

    Laboratoire de Cristallographie et de Modélisation des Matériaux Minéraux et Biologiques, UMR CNRS-Université Henri Poincaré (UHP) 7036.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glyceraldehyde-3-phosphate dehydrogenaseA [auth O], B [auth P], C [auth Q], D [auth R]334N/AMutation(s): 0 
Gene Names: gap
EC: 1.2.1.12
Find proteins for P00362 (Geobacillus stearothermophilus)
Explore P00362 
Go to UniProtKB:  P00362
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
KA [auth R], L [auth O], Q [auth P], Z [auth Q]NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
G3H
Query on G3H

Download Ideal Coordinates CCD File 
JA [auth R], K [auth O], P, Y [auth Q]GLYCERALDEHYDE-3-PHOSPHATE
C3 H7 O6 P
LXJXRIRHZLFYRP-VKHMYHEASA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
CA [auth R] , DA [auth R] , E [auth O] , EA [auth R] , F [auth O] , FA [auth R] , G [auth O] , GA [auth R] , 
CA [auth R],  DA [auth R],  E [auth O],  EA [auth R],  F [auth O],  FA [auth R],  G [auth O],  GA [auth R],  H [auth O],  HA [auth R],  I [auth O],  IA [auth R],  J [auth O],  N [auth P],  O [auth P],  V [auth Q],  W [auth Q],  X [auth Q]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth Q], LA [auth R], M [auth O], MA [auth R], R [auth P], S [auth P], T [auth P], U [auth P]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth Q]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.163 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.67α = 90
b = 122.63β = 111.12
c = 81.79γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
MOLREPphasing
TNTrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata reduction
BUSTER-TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance