1PQH

Serine 25 to Threonine mutation of aspartate decarboxylase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    1PQH, 1PQF, 1PQE, 1PPY, 1PT1, 1PT0, 1PYQ, 1PYU

  • 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 Gly24-->Ser, His11-->Ala, Ser25-->Ala, Ser25-->Cys and Ser25-->Thr mutants ...

    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: 
    • 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
    • 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 2.2A 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 Biol 5: 289

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Aspartate 1-decarboxylase AB143Escherichia coliMutation(s): 2 
Gene Names: panD
EC: 4.1.1.11
Find proteins for P0A790 (Escherichia coli (strain K12))
Explore P0A790 
Go to UniProtKB:  P0A790
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MLA
Query on MLA

Download Ideal Coordinates CCD File 
A, B
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSX
Query on CSX
A,BL-PEPTIDE LINKINGC3 H7 N O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.166 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.153 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.46α = 90
b = 70.46β = 90
c = 215.299γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2015-04-29
    Changes: Non-polymer description