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PDBsum entry 1pyu
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protein ligands Protein-protein interface(s) links
Lyase PDB id
1pyu

 

 

 

 

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JSmol PyMol  
Contents
Protein chains
28 a.a.
92 a.a. *
24 a.a. *
Ligands
SO4 ×2
Waters ×180
* Residue conservation analysis
PDB id:
1pyu
Name: Lyase
Title: Processed aspartate decarboxylase mutant with ser25 mutated to cys
Structure: Aspartate 1-decarboxylase beta chain. Chain: a, c. Synonym: aspartate alpha-decarboxylase. Engineered: yes. Aspartate 1-decarboxylase alfa chain. Chain: b, d. Synonym: aspartate alpha-decarboxylase. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: pand. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
Resolution:
1.90Å     R-factor:   0.174     R-free:   0.196
Authors: F.Schmitzberger,M.L.Kilkenny,C.M.C.Lobley,M.E.Webb,M.Vinkovic, D.Matak-Vinkovic,M.Witty,D.Y.Chirgadze,A.G.Smith,C.Abell, T.L.Blundell
Key ref:
F.Schmitzberger et al. (2003). Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase. EMBO J, 22, 6193-6204. PubMed id: 14633979 DOI: 10.1093/emboj/cdg575
Date:
09-Jul-03     Release date:   18-Nov-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A790  (PAND_ECOLI) -  Aspartate 1-decarboxylase from Escherichia coli (strain K12)
Seq:
Struc: 		126 a.a.
28 a.a.
Protein chains
Pfam   ArchSchema ?
P0A790  (PAND_ECOLI) -  Aspartate 1-decarboxylase from Escherichia coli (strain K12)
Seq:
Struc: 		126 a.a.
92 a.a.*
Protein chain
Pfam   ArchSchema ?
P0A790  (PAND_ECOLI) -  Aspartate 1-decarboxylase from Escherichia coli (strain K12)
Seq:
Struc: 		126 a.a.
24 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B, C, D: E.C.4.1.1.11  - aspartate 1-decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway: 		Coenzyme A Biosynthesis (early stages)
      Reaction: L-aspartate + H+ = beta-alanine + CO2
L-aspartate
 + H(+)
 = beta-alanine
 + CO2
      Cofactor: Pyruvate
Pyruvate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1093/emboj/cdg575 EMBO J 22:6193-6204 (2003)
PubMed id: 14633979  
 
 
Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase.
F.Schmitzberger, M.L.Kilkenny, C.M.Lobley, M.E.Webb, M.Vinkovic, D.Matak-Vinkovic, M.Witty, D.Y.Chirgadze, A.G.Smith, C.Abell, T.L.Blundell.
 
  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.
 
  Selected figure(s)  
 
Figure 1.
Figure 1 The ADC tetramer, viewed with the internal four-fold axis in the plane of the paper, with the secondary structure of each subunit coloured differently. The pyruvoyl group (Pvl-group) and Gly24 of one subunit protomer in the foreground are shown in ball and stick representation (colour scheme as in Figure 4). Figures 1 and 6 were prepared with Molscript (Kraulis, 1991) and rendered in Raster3D (Merritt and Bacon, 1997). 		Figure 2.
Figure 2 Schematic representation of the self-processing reaction, as it is currently understood, applied to ADC. Base 1, acid 1 and base 2 are designated as :B 1, H-A 1 and :B 2, respectively.
 
  The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2003, 22, 6193-6204) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20124698 S.Bale, K.Baba, D.E.McCloskey, A.E.Pegg, and S.E.Ealick (2010).
Complexes of Thermotoga maritimaS-adenosylmethionine decarboxylase provide insights into substrate specificity.
  Acta Crystallogr D Biol Crystallogr, 66, 181-189.
PDB codes: 3iwb 3iwc 3iwd
19997761 S.Bale, and S.E.Ealick (2010).
Structural biology of S-adenosylmethionine decarboxylase.
  Amino Acids, 38, 451-460.  
19609288 K.J.Laiple, T.Härtner, H.P.Fiedler, W.Wohlleben, and T.Weber (2009).
The kirromycin gene cluster of Streptomyces collinus Tü 365 codes for an aspartate-alpha-decarboxylase, KirD, which is involved in the biosynthesis of the precursor beta-alanine.
  J Antibiot (Tokyo), 62, 465-468.  
18391404 E.V.Soriano, D.E.McCloskey, C.Kinsland, A.E.Pegg, and S.E.Ealick (2008).
Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii.
  Acta Crystallogr D Biol Crystallogr, 64, 377-382.
PDB codes: 2qqc 2qqd
18334484 K.Michalska, A.Hernandez-Santoyo, and M.Jaskolski (2008).
The mechanism of autocatalytic activation of plant-type L-asparaginases.
  J Biol Chem, 283, 13388-13397.
PDB code: 3c17
18287282 Y.Sun, and H.C.Guo (2008).
Structural constraints on autoprocessing of the human nucleoporin Nup98.
  Protein Sci, 17, 494-505.
PDB codes: 2q5x 2q5y
17898895 D.E.Scott, A.Ciulli, and C.Abell (2007).
Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.
  Nat Prod Rep, 24, 1009-1026.  
17898894 M.E.Webb, A.Marquet, R.R.Mendel, F.Rébeillé, and A.G.Smith (2007).
Elucidating biosynthetic pathways for vitamins and cofactors.
  Nat Prod Rep, 24, 988.  
16369486 B.Macao, D.G.Johansson, G.C.Hansson, and T.Härd (2006).
Autoproteolysis coupled to protein folding in the SEA domain of the membrane-bound MUC1 mucin.
  Nat Struct Mol Biol, 13, 71-76.
PDB code: 2acm
17001646 G.Gopalan, S.Chopra, A.Ranganathan, and K.Swaminathan (2006).
Crystal structure of uncleaved L-aspartate-alpha-decarboxylase from Mycobacterium tuberculosis.
  Proteins, 65, 796-802.
PDB code: 2c45
15150268 A.V.Toms, C.Kinsland, D.E.McCloskey, A.E.Pegg, and S.E.Ealick (2004).
Evolutionary links as revealed by the structure of Thermotoga maritima S-adenosylmethionine decarboxylase.
  J Biol Chem, 279, 33837-33846.
PDB codes: 1tlu 1tmi
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.

 

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