Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Hetero 8-mer - A4B4 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 31820.07 
• Atom Count: 1799 
• Residue Count: 286 
• Unique protein chains: 2

1PYU

Processed Aspartate Decarboxylase Mutant with Ser25 mutated to Cys

• DOI: 10.2210/pdb1PYU/pdb

• Classification: LYASE
• Organism(s): Escherichia coli (strain K12)
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2003-07-09 Released: 2003-11-18 
• Deposition Author(s): 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.196 
• R-Value Work: 0.173 

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

• PubMed: 14633979 
• DOI: 10.1093/emboj/cdg575
• Primary Citation of Related Structures:  
  1PYQ, 1PT1, 1PT0, 1PQH, 1PQF, 1PQE, 1PPY
• 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 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.

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Related Citations: 

• 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.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
• 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




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Organizational Affiliation: 

Department of Biochemistry, 80 Tennis Court Road, Cambridge CB2 1GA, UK. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Aspartate 1-decarboxylase beta chain	A, C	41	Escherichia coli (strain K12)	Mutation(s): 0  Gene Names: panD EC: 4.1.1.11
Find proteins for P0A790 (Escherichia coli (strain K12)) Go to UniProtKB:  P0A790

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Aspartate 1-decarboxylase alfa chain	B, D	102	Escherichia coli (strain K12)	Mutation(s): 1  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
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	B, D	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.196 
• R-Value Work: 0.173 
• Space Group: P 6₁ 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 70.787	α = 90.00
b = 70.787	β = 90.00
c = 217.121	γ = 120.00

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	phasing
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-09 
• Released Date: 2003-11-18 
• Deposition Author(s): 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.

Revision History 

• Version 1.0: 2003-11-18
  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