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PDBsum entry 1aw8

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protein Protein-protein interface(s) links
Decarboxylase PDB id
1aw8
Jmol
Contents
Protein chains
24 a.a.
92 a.a. *
Waters ×98
* Residue conservation analysis
PDB id:
1aw8
Name: Decarboxylase
Title: Pyruvoyl dependent aspartate decarboxylase
Structure: L-aspartate-alpha-decarboxylase. Chain: a, d. Engineered: yes. L-aspartate-alpha-decarboxylase. Chain: b, e. Engineered: yes. Other_details: microheterogeneity at residue b25
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562
Biol. unit: Tetramer (from PDB file)
Resolution:
2.20Å     R-factor:   0.200     R-free:   0.239
Authors: A.Albert,V.Dhanaraj,U.Genschel,G.Khan,M.K.Ramjee,R.Pulido, B.L.Sybanda,F.Von Delf,M.Witty,T.L.Blundell,A.G.Smith,C.Abe
Key ref: A.Albert et al. (1998). Crystal structure of aspartate decarboxylase at 2.2 A resolution provides evidence for an ester in protein self-processing. Nat Struct Biol, 5, 289-293. PubMed id: 9546220
Date:
12-Oct-97     Release date:   29-Apr-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0A790  (PAND_ECOLI) -  Aspartate 1-decarboxylase
Seq:
Struc:
126 a.a.
24 a.a.
Protein chains
Pfam   ArchSchema ?
P0A790  (PAND_ECOLI) -  Aspartate 1-decarboxylase
Seq:
Struc:
126 a.a.
92 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, D, E: E.C.4.1.1.11  - Aspartate 1-decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Coenzyme A Biosynthesis (early stages)
      Reaction: L-aspartate = beta-alanine + CO2
L-aspartate
= beta-alanine
+ CO(2)
      Cofactor: Pyruvate
Pyruvate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     alanine biosynthetic process   1 term 
  Biochemical function     aspartate 1-decarboxylase activity     1 term  

 

 
    reference    
 
 
Nat Struct Biol 5:289-293 (1998)
PubMed id: 9546220  
 
 
Crystal structure of aspartate decarboxylase at 2.2 A resolution provides evidence for an ester in protein self-processing.
A.Albert, V.Dhanaraj, U.Genschel, G.Khan, M.K.Ramjee, R.Pulido, B.L.Sibanda, F.von Delft, M.Witty, T.L.Blundell, A.G.Smith, C.Abell.
 
  ABSTRACT  
 
The structure of L-aspartate-alpha-decarboxylase from E. coli has been determined at 2.2 A resolution. The enzyme is a tetramer with pseudofour-fold rotational symmetry. The subunits are six-stranded beta-barrels capped by small alpha-helices at each end. The active sites are located between adjacent subunits. The electron density provides evidence for catalytic pyruvoyl groups at three active sites and an ester at the fourth. The ester is an intermediate in the autocatalytic self-processing leading to formation of the pyruvoyl group. This unprecedented structure provides novel insights into the general phenomenon of protein processing.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21208300 H.Trip, N.L.Mulder, F.P.Rattray, and J.S.Lolkema (2011).
HdcB, a novel enzyme catalysing maturation of pyruvoyl-dependent histidine decarboxylase.
  Mol Microbiol, 79, 861-871.  
20645337 J.de Villiers, L.Koekemoer, and E.Strauss (2010).
3-Fluoroaspartate and pyruvoyl-dependant aspartate decarboxylase: exploiting the unique characteristics of fluorine to probe reactivity and binding.
  Chemistry, 16, 10030-10041.  
19997761 S.Bale, and S.E.Ealick (2010).
Structural biology of S-adenosylmethionine decarboxylase.
  Amino Acids, 38, 451-460.  
19353301 W.M.Fouad, and F.Altpeter (2009).
Transplastomic expression of bacterial L-aspartate-alpha-decarboxylase enhances photosynthesis and biomass production in response to high temperature stress.
  Transgenic Res, 18, 707-718.  
17898895 D.E.Scott, A.Ciulli, and C.Abell (2007).
Coenzyme biosynthesis: enzyme mechanism, structure and inhibition.
  Nat Prod Rep, 24, 1009-1026.  
17898893 G.L.Holliday, J.M.Thornton, A.Marquet, A.G.Smith, F.Rébeillé, R.Mendel, H.L.Schubert, A.D.Lawrence, and M.J.Warren (2007).
Evolution of enzymes and pathways for the biosynthesis of cofactors.
  Nat Prod Rep, 24, 972-987.  
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.  
17600793 Z.Q.Beck, D.A.Burr, and D.H.Sherman (2007).
Characterization of the beta-methylaspartate-alpha-decarboxylase (CrpG) from the cryptophycin biosynthetic pathway.
  Chembiochem, 8, 1373-1375.  
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
16525887 W.M.Fouad, and B.Rathinasabapathi (2006).
Expression of bacterial L-aspartate-alpha-decarboxylase in tobacco increases beta-alanine and pantothenate levels and improves thermotolerance.
  Plant Mol Biol, 60, 495-505.  
16267872 C.T.Walsh, S.Garneau-Tsodikova, and G.J.Gatto (2005).
Protein posttranslational modifications: the chemistry of proteome diversifications.
  Angew Chem Int Ed Engl, 44, 7342-7372.  
15987679 F.Levitin, O.Stern, M.Weiss, C.Gil-Henn, R.Ziv, Z.Prokocimer, N.I.Smorodinsky, D.B.Rubinstein, and D.H.Wreschner (2005).
The MUC1 SEA module is a self-cleaving domain.
  J Biol Chem, 280, 33374-33386.  
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
15288250 D.A.Erlanson, and S.K.Hansen (2004).
Making drugs on proteins: site-directed ligand discovery for fragment-based lead assembly.
  Curr Opin Chem Biol, 8, 399-406.  
14675432 H.H.Ottenhof, J.L.Ashurst, H.M.Whitney, S.A.Saldanha, F.Schmitzberger, H.S.Gweon, T.L.Blundell, C.Abell, and A.G.Smith (2004).
Organisation of the pantothenate (vitamin B5) biosynthesis pathway in higher plants.
  Plant J, 37, 61-72.  
14633979 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, and T.L.Blundell (2003).
Structural constraints on protein self-processing in L-aspartate-alpha-decarboxylase.
  EMBO J, 22, 6193-6204.
PDB codes: 1ppy 1pqe 1pqf 1pqh 1pt0 1pt1 1pyq 1pyu
12906829 F.von Delft, T.Inoue, S.A.Saldanha, H.H.Ottenhof, F.Schmitzberger, L.M.Birch, V.Dhanaraj, M.Witty, A.G.Smith, T.L.Blundell, and C.Abell (2003).
Structure of E. coli ketopantoate hydroxymethyl transferase complexed with ketopantoate and Mg2+, solved by locating 160 selenomethionine sites.
  Structure, 11, 985-996.
PDB code: 1m3u
12906824 N.Manoj, E.Strauss, T.P.Begley, and S.E.Ealick (2003).
Structure of human phosphopantothenoylcysteine synthetase at 2.3 A resolution.
  Structure, 11, 927-936.
PDB code: 1p9o
12906830 X.Qian, C.Guan, and H.C.Guo (2003).
A dual role for an aspartic acid in glycosylasparaginase autoproteolysis.
  Structure, 11, 997.
PDB codes: 1p4k 1p4v
11422384 B.Bednarski, J.R.Andreesen, and A.Pich (2001).
In vitro processing of the proproteins GrdE of protein B of glycine reductase and PrdA of D-proline reductase from Clostridium sticklandii: formation of a pyruvoyl group from a cysteine residue.
  Eur J Biochem, 268, 3538-3544.  
10966466 H.Paulus (2000).
Protein splicing and related forms of protein autoprocessing.
  Annu Rev Biochem, 69, 447-496.  
10574985 H.Xiong, and A.E.Pegg (1999).
Mechanistic studies of the processing of human S-adenosylmethionine decarboxylase proenzyme. Isolation of an ester intermediate.
  J Biol Chem, 274, 35059-35066.  
10378277 J.L.Ekstrom, I.I.Mathews, B.A.Stanley, A.E.Pegg, and S.E.Ealick (1999).
The crystal structure of human S-adenosylmethionine decarboxylase at 2.25 A resolution reveals a novel fold.
  Structure, 7, 583-595.
PDB code: 1jen
  10103247 N.Dusch, A.Pühler, and J.Kalinowski (1999).
Expression of the Corynebacterium glutamicum panD gene encoding L-aspartate-alpha-decarboxylase leads to pantothenate overproduction in Escherichia coli.
  Appl Environ Microbiol, 65, 1530-1539.  
10490104 Q.Xu, D.Buckley, C.Guan, and H.C.Guo (1999).
Structural insights into the mechanism of intramolecular proteolysis.
  Cell, 98, 651-661.
PDB codes: 9gaa 9gac 9gaf
10368289 R.M.Castillo, K.Mizuguchi, V.Dhanaraj, A.Albert, T.L.Blundell, and A.G.Murzin (1999).
A six-stranded double-psi beta barrel is shared by several protein superfamilies.
  Structure, 7, 227-236.  
10085076 U.C.Kabisch, A.Gräntzdörffer, A.Schierhorn, K.P.Rücknagel, J.R.Andreesen, and A.Pich (1999).
Identification of D-proline reductase from Clostridium sticklandii as a selenoenzyme and indications for a catalytically active pyruvoyl group derived from a cysteine residue by cleavage of a proprotein.
  J Biol Chem, 274, 8445-8454.  
9546209 F.B.Perler (1998).
Breaking up is easy with esters.
  Nat Struct Biol, 5, 249-252.  
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 code is shown on the right.