1PT0

Unprocessed Pyruvoyl Dependent Aspartate Decarboxylase with an Alanine insertion at position 26


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase

Schmitzberger, F.Kilkenny, M.L.Lobley, C.M.C.Webb, M.E.Vinkovic, M.Matak-Vinkovic, D.Witty, M.Chirgadze, D.Y.Smith, A.G.Abell, C.Blundell, T.L.

(2003) Embo J. 22: 6193-6204

  • DOI: 10.1093/emboj/cdg575
  • Primary Citation of Related Structures:  1PPY, 1PQE, 1PQF, 1PQH, 1PT1, 1PYQ, 1PYU
  • Also Cited By: 2C45

  • PubMed Abstract: 
  • Aspartate decarboxylase, which is translated as a pro-protein, undergoes intramolecular self-cleavage at Gly24-Ser25. We have determined the crystal structures of an unprocessed native precursor, in addition to Ala24 insertion, Ala26 insertion and Gl ...

    Aspartate decarboxylase, which is translated as a pro-protein, undergoes intramolecular self-cleavage at Gly24-Ser25. We have determined the crystal structures of an unprocessed native precursor, in addition to Ala24 insertion, Ala26 insertion and Gly24-->Ser, His11-->Ala, Ser25-->Ala, Ser25-->Cys and Ser25-->Thr mutants. Comparative analyses of the cleavage site reveal specific conformational constraints that govern self-processing and demonstrate that considerable rearrangement must occur. We suggest that Thr57 Ogamma and a water molecule form an 'oxyanion hole' that likely stabilizes the proposed oxyoxazolidine intermediate. Thr57 and this water molecule are probable catalytic residues able to support acid-base catalysis. The conformational freedom in the loop preceding the cleavage site appears to play a determining role in the reaction. The molecular mechanism of self-processing, presented here, emphasizes the importance of stabilization of the oxyoxazolidine intermediate. Comparison of the structural features shows significant similarity to those in other self-processing systems, and suggests that models of the cleavage site of such enzymes based on Ser-->Ala or Ser-->Thr mutants alone may lead to erroneous interpretations of the mechanism.


    Related Citations: 
    • Escherichia coli L-aspartate-alpha-decarboxylase: preprotein processing and observation of reaction intermediates by electrospray mass spectrometry
      Ramjee, M.K.,Genschel, U.,Abell, C.,Smith, A.G.
      (1997) Biochem.J. 323: 661
    • Crystal structure of aspartate decarboxylase at 2.2 A resolution provides evidence for an ester in protein self-processing
      Albert, A.,Dhanaraj, V.,Genschel, U.,Khan, G.,Ramjee, M.K.,Pulido, R.,Sibanda, B.L.,von Delft, F.,Witty, M.,Blundell, T.L.,Smith, A.G.,Abell, C.
      (1998) Nat.Struct.Mol.Biol. 5: 289
    • Purification and properties of L-Aspartate-alpha-decarboxylase, an enzyme that catalyzes the formation of beta-alanine in Escherichia coli
      Williamson, J.M.,Brown, G.M.
      (1979) J.Biol.Chem. 254: 8074


    Organizational Affiliation

    Department of Biochemistry, 80 Tennis Court Road, Cambridge CB2 1GA, UK. florian@cryst.bioc.cam.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aspartate 1-decarboxylase
A, B
144Escherichia coli (strain K12)Gene Names: panD
EC: 4.1.1.11
Find proteins for P0A790 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A790
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.174 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 70.935α = 90.00
b = 70.935β = 90.00
c = 217.741γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
REFMACrefinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-11-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Derived calculations, Version format compliance