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PDBsum entry 1pox
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protein ligands metals Protein-protein interface(s) links
Oxidoreductase(oxygen as acceptor) PDB id
1pox

 

 

 

 

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Contents
Protein chains
585 a.a. *
Ligands
TPP ×2
FAD ×2
GOL ×2
Metals
_MG ×2
_NA ×2
Waters ×739
* Residue conservation analysis
PDB id:
1pox
Name: Oxidoreductase(oxygen as acceptor)
Title: The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from lactobacillus plantarum
Structure: Pyruvate oxidase. Chain: a, b. Engineered: yes
Source: Lactobacillus plantarum. Organism_taxid: 1590
Biol. unit: Tetramer (from PQS)
Resolution:
2.10Å     R-factor:   0.162    
Authors: Y.A.Muller,G.E.Schulz
Key ref: Y.A.Muller et al. (1994). The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from Lactobacillus plantarum. J Mol Biol, 237, 315-335. PubMed id: 8145244
Date:
09-Nov-93     Release date:   31-Jan-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
P37063  (POXB_LACPL) -  Pyruvate oxidase from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
Seq:
Struc: 		 
Seq:
Struc: 		603 a.a.
585 a.a.*
Key:    Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.1.2.3.3  - pyruvate oxidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: pyruvate + phosphate + O2 + H+ = acetyl phosphate + H2O2 + CO2
pyruvate
 + phosphate
 + O2
 + H(+)
Bound ligand (Het Group name = GOL)
matches with 71.43% similarity 		= acetyl phosphate
 + H2O2
 + CO2
      Cofactor: FAD; Thiamine diphosphate
FAD
Bound ligand (Het Group name = FAD) corresponds exactly
Thiamine diphosphate
Bound ligand (Het Group name = TPP) corresponds exactly
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
J Mol Biol 237:315-335 (1994)
PubMed id: 8145244  
 
 
The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from Lactobacillus plantarum.
Y.A.Muller, G.Schumacher, R.Rudolph, G.E.Schulz.
 
  ABSTRACT  
 
The crystal structure of pyruvate oxidase (EC 1.2.3.3) from Lactobacillus plantarum stabilized by three point mutations has been refined at 2.1 A resolution using the simulated annealing method. Based on 87,775 independent reflections in the resolution range 10 to 2.1 A, a final R-factor of 16.2% was obtained at good model geometry. The wild-type enzyme crystallizes isomorphously with the stabilized enzyme and has been analyzed at 2.5 A resolution. Pyruvate oxidase is a homotetramer with point group symmetry D2. One 2-fold axis is crystallographic, the others are local. The crystallographic asymmetric unit contains two subunits, and the model consists of the two polypeptide chains (residues 9 through 593), two FAD, two ThDP*Mg2+ and 739 water molecules. Each subunit has three domains; the CORE domain, the FAD domain and the ThDP domain. The FAD-binding chain fold is different from those of other known flavoproteins, whereas the ThDP-binding chain fold resembles the corresponding folds of the two other ThDP enzymes whose structure is known, transketolase and pyruvate decarboxylase. The peptide environment most likely forces the pyrimidine ring of ThDP into an unusual tautomeric form, which is required for catalysis. The structural differences between the wild-type and the stabilized enzyme are small. All three point mutations are at or near to the subunit interfaces, indicating that they stabilize the quarternary structure as had been deduced from reconstitution experiments.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20847003 L.Chen, X.Ge, Y.Dou, X.Wang, J.R.Patel, and P.Xu (2011).
Identification of hydrogen peroxide production-related genes in Streptococcus sanguinis and their functional relationship with pyruvate oxidase.
  Microbiology, 157, 13-20.  
  20975902 A.Shrestha, S.Dhamwichukorn, and E.Jenwitheesuk (2010).
Modeling of pyruvate decarboxylases from ethanol producing bacteria.
  Bioinformation, 4, 378-384.  
20099870 X.Y.Pei, K.M.Erixon, B.F.Luisi, and F.J.Leeper (2010).
Structural insights into the prereaction state of pyruvate decarboxylase from Zymomonas mobilis .
  Biochemistry, 49, 1727-1736.
PDB codes: 2wva 2wvg 2wvh
18430561 E.Akyilmaz, and E.Yorganci (2008).
A novel biosensor based on activation effect of thiamine on the activity of pyruvate oxidase.
  Biosens Bioelectron, 23, 1874-1877.  
18058864 M.Alstrup Lie, and B.Schiøtt (2008).
A DFT study of solvation effects on the tautomeric equilibrium and catalytic ylide generation of thiamin models.
  J Comput Chem, 29, 1037-1047.  
18988747 P.Neumann, A.Weidner, A.Pech, M.T.Stubbs, and K.Tittmann (2008).
Structural basis for membrane binding and catalytic activation of the peripheral membrane enzyme pyruvate oxidase from Escherichia coli.
  Proc Natl Acad Sci U S A, 105, 17390-17395.
PDB codes: 3ey9 3eya
18621675 W.Gong, B.Hao, Z.Wei, D.J.Ferguson, T.Tallant, J.A.Krzycki, and M.K.Chan (2008).
Structure of the alpha2epsilon2 Ni-dependent CO dehydrogenase component of the Methanosarcina barkeri acetyl-CoA decarbonylase/synthase complex.
  Proc Natl Acad Sci U S A, 105, 9558-9563.
PDB code: 3cf4
  18007037 E.C.Juan, M.M.Hoque, M.T.Hossain, T.Yamamoto, S.Imamura, K.Suzuki, T.Sekiguchi, and A.Takénaka (2007).
The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 900-907.
PDB codes: 1v5f 1v5g 2dji
17391016 H.Xie, S.Vucetic, L.M.Iakoucheva, C.J.Oldfield, A.K.Dunker, Z.Obradovic, and V.N.Uversky (2007).
Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins.
  J Proteome Res, 6, 1917-1932.  
16699828 J.A.McCourt, and R.G.Duggleby (2006).
Acetohydroxyacid synthase and its role in the biosynthetic pathway for branched-chain amino acids.
  Amino Acids, 31, 173-210.  
16452416 M.E.Schreiner, C.Riedel, J.Holátko, M.Pátek, and B.J.Eikmanns (2006).
Pyruvate:quinone oxidoreductase in Corynebacterium glutamicum: molecular analysis of the pqo gene, significance of the enzyme, and phylogenetic aspects.
  J Bacteriol, 188, 1341-1350.  
17012588 P.Goffin, L.Muscariello, F.Lorquet, A.Stukkens, D.Prozzi, M.Sacco, M.Kleerebezem, and P.Hols (2006).
Involvement of pyruvate oxidase activity and acetate production in the survival of Lactobacillus plantarum during the stationary phase of aerobic growth.
  Appl Environ Microbiol, 72, 7933-7940.  
15659664 M.E.Schreiner, and B.J.Eikmanns (2005).
Pyruvate:quinone oxidoreductase from Corynebacterium glutamicum: purification and biochemical characterization.
  J Bacteriol, 187, 862-871.  
15752351 R.Golbik, L.E.Meshalkina, T.Sandalova, K.Tittmann, E.Fiedler, H.Neef, S.König, R.Kluger, G.A.Kochetov, G.Schneider, and G.Hübner (2005).
Effect of coenzyme modification on the structural and catalytic properties of wild-type transketolase and of the variant E418A from Saccharomyces cerevisiae.
  FEBS J, 272, 1326-1342.  
15175288 F.Lorquet, P.Goffin, L.Muscariello, J.B.Baudry, V.Ladero, M.Sacco, M.Kleerebezem, and P.Hols (2004).
Characterization and functional analysis of the poxB gene, which encodes pyruvate oxidase in Lactobacillus plantarum.
  J Bacteriol, 186, 3749-3759.  
15044456 S.Engel, M.Vyazmensky, M.Vinogradov, D.Berkovich, A.Bar-Ilan, U.Qimron, Y.Rosiansky, Z.Barak, and D.M.Chipman (2004).
Role of a conserved arginine in the mechanism of acetohydroxyacid synthase: catalysis of condensation with a specific ketoacid substrate.
  J Biol Chem, 279, 24803-24812.  
14557277 S.S.Pang, R.G.Duggleby, R.L.Schowen, and L.W.Guddat (2004).
The crystal structures of Klebsiella pneumoniae acetolactate synthase with enzyme-bound cofactor and with an unusual intermediate.
  J Biol Chem, 279, 2242-2253.
PDB codes: 1n0h 1ozf 1ozg 1ozh
12651851 E.M.Ciszak, L.G.Korotchkina, P.M.Dominiak, S.Sidhu, and M.S.Patel (2003).
Structural basis for flip-flop action of thiamin pyrophosphate-dependent enzymes revealed by human pyruvate dehydrogenase.
  J Biol Chem, 278, 21240-21246.
PDB code: 1ni4
14674755 G.Wille, M.Ritter, R.Friedemann, W.Mäntele, and G.Hübner (2003).
Redox-triggered FTIR difference spectra of FAD in aqueous solution and bound to flavoproteins.
  Biochemistry, 42, 14814-14821.  
14621995 M.Bhasin, J.L.Billinsky, and D.R.Palmer (2003).
Steady-state kinetics and molecular evolution of Escherichia coli MenD [(1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase], an anomalous thiamin diphosphate-dependent decarboxylase-carboligase.
  Biochemistry, 42, 13496-13504.  
12876343 M.Blaesse, T.Kupke, R.Huber, and S.Steinbacher (2003).
Structure of MrsD, an FAD-binding protein of the HFCD family.
  Acta Crystallogr D Biol Crystallogr, 59, 1414-1421.
PDB code: 1p3y
12496246 S.S.Pang, L.W.Guddat, and R.G.Duggleby (2003).
Molecular basis of sulfonylurea herbicide inhibition of acetohydroxyacid synthase.
  J Biol Chem, 278, 7639-7644.
PDB code: 1n0h
11805110 C.A.Haynes, R.L.Koder, A.F.Miller, and D.W.Rodgers (2002).
Structures of nitroreductase in three states: effects of inhibitor binding and reduction.
  J Biol Chem, 277, 11513-11520.
PDB codes: 1kqb 1kqc 1kqd
11435118 L.J.Baker, J.A.Dorocke, R.A.Harris, and D.E.Timm (2001).
The crystal structure of yeast thiamin pyrophosphokinase.
  Structure, 9, 539-546.
PDB code: 1ig0
11514662 O.Dym, and D.Eisenberg (2001).
Sequence-structure analysis of FAD-containing proteins.
  Protein Sci, 10, 1712-1728.  
10617618 D.I.Svergun, M.V.Petoukhov, M.H.Koch, and S.König (2000).
Crystal versus solution structures of thiamine diphosphate-dependent enzymes.
  J Biol Chem, 275, 297-302.  
10978159 K.Tittmann, R.Golbik, S.Ghisla, and G.Hübner (2000).
Mechanism of elementary catalytic steps of pyruvate oxidase from Lactobacillus plantarum.
  Biochemistry, 39, 10747-10754.  
  11087175 P.A.Herring, and J.H.Jackson (2000).
Theoretical indicators of enzyme reaction specificity from conserved information in amino acid sidechains.
  Microb Comp Genomics, 5, 75-87.  
10673423 S.A.White, S.J.Peake, S.McSweeney, G.Leonard, N.P.Cotton, and J.B.Jackson (2000).
The high-resolution structure of the NADP(H)-binding component (dIII) of proton-translocating transhydrogenase from human heart mitochondria.
  Structure, 8, 1.
PDB code: 1djl
  10595539 B.W.Lennon, C.H.Williams, and M.L.Ludwig (1999).
Crystal structure of reduced thioredoxin reductase from Escherichia coli: structural flexibility in the isoalloxazine ring of the flavin adenine dinucleotide cofactor.
  Protein Sci, 8, 2366-2379.
PDB code: 1cl0
10350464 H.J.Chiu, J.J.Reddick, T.P.Begley, and S.E.Ealick (1999).
Crystal structure of thiamin phosphate synthase from Bacillus subtilis at 1.25 A resolution.
  Biochemistry, 38, 6460-6470.
PDB code: 2tps
10607667 M.H.Charon, A.Volbeda, E.Chabriere, L.Pieulle, and J.C.Fontecilla-Camps (1999).
Structure and electron transfer mechanism of pyruvate:ferredoxin oxidoreductase.
  Curr Opin Struct Biol, 9, 663-669.  
9582325 K.Tittmann, D.Proske, M.Spinka, S.Ghisla, R.Rudolph, G.Hübner, and G.Kern (1998).
Activation of thiamin diphosphate and FAD in the phosphatedependent pyruvate oxidase from Lactobacillus plantarum.
  J Biol Chem, 273, 12929-12934.  
9665697 M.S.Hasson, A.Muscate, M.J.McLeish, L.S.Polovnikova, J.A.Gerlt, G.L.Kenyon, G.A.Petsko, and D.Ringe (1998).
The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes.
  Biochemistry, 37, 9918-9930.
PDB code: 1bfd
9351807 Y.A.Muller, H.W.Christinger, B.A.Keyt, and A.M.de Vos (1997).
The crystal structure of vascular endothelial growth factor (VEGF) refined to 1.93 A resolution: multiple copy flexibility and receptor binding.
  Structure, 5, 1325-1338.
PDB code: 2vpf
9305946 Y.Y.Chang, and J.E.Cronan (1997).
Sulfhydryl chemistry detects three conformations of the lipid binding region of Escherichia coli pyruvate oxidase.
  Biochemistry, 36, 11564-11573.  
8973202 M.Ibdah, A.Bar-Ilan, O.Livnah, J.V.Schloss, Z.Barak, and D.M.Chipman (1996).
Homology modeling of the structure of bacterial acetohydroxy acid synthase and examination of the active site by site-directed mutagenesis.
  Biochemistry, 35, 16282-16291.  
8756689 M.Vyazmensky, C.Sella, Z.Barak, and D.M.Chipman (1996).
Isolation and characterization of subunits of acetohydroxy acid synthase isozyme III and reconstitution of the holoenzyme.
  Biochemistry, 35, 10339-10346.  
7713884 Y.Y.Chang, and J.E.Cronan (1995).
Detection by site-specific disulfide cross-linking of a conformational change in binding of Escherichia coli pyruvate oxidase to lipid bilayers.
  J Biol Chem, 270, 7896-7901.  
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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