spacer
spacer

PDBsum entry 1pya

Go to PDB code: 
protein Protein-protein interface(s) links
Carboxy-lyase PDB id
1pya
Jmol
Contents
Protein chains
81 a.a. *
229 a.a. *
Waters ×1413
* Residue conservation analysis
PDB id:
1pya
Name: Carboxy-lyase
Title: Refined structure of the pyruvoyl-dependent histidine decarboxylase from lactobacillus 30a
Structure: Pyruvoyl-dependent histidine decarboxylase (l- histidine carboxylase). Chain: a, c, e. Engineered: yes. Pyruvoyl-dependent histidine decarboxylase (l- histidine carboxylase). Chain: b, d, f. Engineered: yes
Source: Lactobacillus sp. 30a. Organism_taxid: 1593. Strain: 30a. Strain: 30a
Biol. unit: Hexamer (from PQS)
Resolution:
2.50Å     R-factor:   0.150    
Authors: T.Gallagher,D.A.Rozwarski,S.R.Ernst,M.L.Hackert
Key ref: T.Gallagher et al. (1993). Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a. J Mol Biol, 230, 516-528. PubMed id: 8464063 DOI: 10.1006/jmbi.1993.1168
Date:
18-Dec-92     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00862  (DCHS_LACS3) -  Histidine decarboxylase proenzyme
Seq:
Struc:
311 a.a.
81 a.a.
Protein chains
Pfam   ArchSchema ?
P00862  (DCHS_LACS3) -  Histidine decarboxylase proenzyme
Seq:
Struc:
311 a.a.
229 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, F: E.C.4.1.1.22  - Histidine decarboxylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-histidine = histamine + CO2
L-histidine
= histamine
+ CO(2)
      Cofactor: Pyruvate or pyridoxal 5'-phosphate
Pyruvate
or pyridoxal 5'-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     cellular amino acid metabolic process   2 terms 
  Biochemical function     carboxy-lyase activity     2 terms  

 

 
    reference    
 
 
DOI no: 10.1006/jmbi.1993.1168 J Mol Biol 230:516-528 (1993)
PubMed id: 8464063  
 
 
Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a.
T.Gallagher, D.A.Rozwarski, S.R.Ernst, M.L.Hackert.
 
  ABSTRACT  
 
The crystal structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a has been refined to an R-value of 0.15 (for the 5.0 to 2.5 A resolution shell) and 0.17 (for the 10.0 to 2.5 A resolution shell). A description of the overall structure is presented, focusing on secondary structure and subunit association. The enzyme is a hexamer of alpha beta subunits. Separate alpha and beta-chains arise from an autocatalytic cleavage reaction between two serine residues, which results in the pyruvoyl cofactor. The central core of the alpha beta subunit is a beta-sandwich which consists of two face-to-face three-stranded antiparallel beta-sheets, flanked by alpha-helices on each side. The beta-sandwich creates a stable fold that allows conformational strain to be introduced across an internal cleavage region between the alpha and beta chains and places the pyruvoyl cofactor in a position for efficient electron withdrawal from the substrate. Three alpha beta subunits are related by a molecular three-fold symmetry axis to form a trimer whose interfaces have complementary surfaces and extensive molecular interactions. Each of the interfaces contains an active site and a solvent channel that leads from the active site to the exterior of the molecule. The trimers are related by a crystallographic two-fold symmetry axis to form the hexamer with an overall dumbbell shape. The interface between trimers has few molecular interactions.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21236322 K.J.Yokoi, Y.Harada, K.Shozen, M.Satomi, A.Taketo, and K.Kodaira (2011).
Characterization of the histidine decarboxylase gene of Staphylococcus epidermidis TYH1 coded on the staphylococcal cassette chromosome.
  Gene, 477, 32-41.  
20640870 S.C.Davis, S.Clark, J.R.Hayes, T.L.Green, and C.A.Gruetter (2011).
Up-regulation of histidine decarboxylase expression and histamine content in B16F10 murine melanoma cells.
  Inflamm Res, 60, 55-61.  
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.  
18198876 J.Crugeiras, A.Rios, E.Riveiros, T.L.Amyes, and J.P.Richard (2008).
Glycine enolates: the effect of formation of iminium ions to simple ketones on alpha-amino carbon acidity and a comparison with pyridoxal iminium ions.
  J Am Chem Soc, 130, 2041-2050.  
15746344 P.M.Lucas, W.A.Wolken, O.Claisse, J.S.Lolkema, and A.Lonvaud-Funel (2005).
Histamine-producing pathway encoded on an unstable plasmid in Lactobacillus hilgardii 0006.
  Appl Environ Microbiol, 71, 1417-1424.  
15281117 A.Barzilai, S.Kumar, H.Wolfson, and R.Nussinov (2004).
Potential folding-function interrelationship in proteins.
  Proteins, 56, 635-649.  
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
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
11835507 S.Worley, E.Schelp, A.F.Monzingo, S.Ernst, and J.D.Robertus (2002).
Structure and cooperativity of a T-state mutant of histidine decarboxylase from Lactobacillus 30a.
  Proteins, 46, 321-329.
PDB codes: 1ibt 1ibu 1ibv 1ibw
11578924 L.Poppe (2001).
Methylidene-imidazolone: a novel electrophile for substrate activation.
  Curr Opin Chem Biol, 5, 512-524.  
10906409 F.S.Tahanejad, H.Naderi-Manesh, B.Habibinejad, and M.Mahmoudian (2000).
Homology-based molecular modelling of PLP-dependent histidine decarboxylase from Mmorganella morganii.
  Eur J Med Chem, 35, 567-576.  
10966466 H.Paulus (2000).
Protein splicing and related forms of protein autoprocessing.
  Annu Rev Biochem, 69, 447-496.  
10903941 N.M.Okeley, and W.A.van der Donk (2000).
Novel cofactors via post-translational modifications of enzyme active sites.
  Chem Biol, 7, R159-R171.  
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
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
9546209 F.B.Perler (1998).
Breaking up is easy with esters.
  Nat Struct Biol, 5, 249-252.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9353291 H.Xiong, B.A.Stanley, B.L.Tekwani, and A.E.Pegg (1997).
Processing of mammalian and plant S-adenosylmethionine decarboxylase proenzymes.
  J Biol Chem, 272, 28342-28348.  
8702788 T.W.Hamelryck, M.H.Dao-Thi, F.Poortmans, M.J.Chrispeels, L.Wyns, and R.Loris (1996).
The crystallographic structure of phytohemagglutinin-L.
  J Biol Chem, 271, 20479-20485.
PDB code: 1fat
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.