DB code: T00237

CATH domain 3.40.50.970 : Rossmann fold Catalytic domain
3.40.50.1220 : Rossmann fold Catalytic domain
3.40.50.970 : Rossmann fold Catalytic domain
E.C. 1.2.3.3
CSA 1pow
M-CSA 1pow
MACiE M0274

CATH domain Related DB codes (homologues)
3.40.50.970 : Rossmann fold T00210 T00230
3.40.50.1220 : Rossmann fold M00162 M00161 T00230

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P37063 Pyruvate oxidase
EC 1.2.3.3
Pyruvic oxidase
POX
YP_004891064.1 (Protein)
NC_004567.2 (DNA/RNA sequence)
PF02775 (TPP_enzyme_C)
PF00205 (TPP_enzyme_M)
PF02776 (TPP_enzyme_N)
[Graphical View]

KEGG enzyme name
pyruvate oxidase
pyruvic oxidase
phosphate-dependent pyruvate oxidase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P37063 POXB_LACPL Pyruvate + phosphate + O(2) = acetyl phosphate + CO(2) + H(2)O(2). Homotetramer. Binds 1 FAD per subunit. Binds 1 magnesium ion per subunit. Binds 1 thiamine pyrophosphate per subunit.

KEGG Pathways
Map code Pathways E.C.
MAP00620 Pyruvate metabolism

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00016 C00068 C00305 C00022 C00009 C00007 C00227 C00011 C00027
E.C.
Compound FAD Thiamine diphosphate Magnesium Pyruvate Orthophosphate O2 Acetyl phosphate CO2 H2O2
Type amide group,amine group,aromatic ring (only carbon atom),aromatic ring (with nitrogen atoms),carbohydrate,nucleotide amine group,aromatic ring (with nitrogen atoms),phosphate group/phosphate ion divalent metal (Ca2+, Mg2+) carbohydrate,carboxyl group phosphate group/phosphate ion others carbohydrate,phosphate group/phosphate ion others others
ChEBI 16238
9532
18420
32816
26078
27140
26689
15379
15350
16526
16240
PubChem 643975
1132
888
1060
22486802
1004
977
186
280
784
22326046
1powA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1powB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1poxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1poxB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1y9dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1y9dB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1y9dC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1y9dD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Analogue:SO4 Unbound Unbound Unbound Unbound
1powA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1powB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1poxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1poxB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:FAD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1y9dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:FAD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1y9dB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:FAD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1y9dC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:FAD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1y9dD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Analogue:FAD Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1powA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:TPP Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound
1powB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:TPP Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound
1poxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:TPP Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound
1poxB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:TPP Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound
1y9dA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:TPP Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound
1y9dB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:TPP Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound
1y9dC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:TPP Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound
1y9dD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Bound:TPP Bound:_MG Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P37063 & literature [5], [8], [10]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1powA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 59
1powB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 59
1poxA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 59 mutant P178S, S188N
1poxB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 59 mutant P178S, S188N
1y9dA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 59
1y9dB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 59
1y9dC01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 59
1y9dD01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 59
1powA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 264
1powB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 264
1poxA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 264
1poxB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 264
1y9dA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 264 mutant V265A
1y9dB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 264 mutant V265A
1y9dC02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 264 mutant V265A
1y9dD02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ARG 264 mutant V265A
1powA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 479;GLU 483 ASP 447;ASN 474;GLN 476(Magnesium binding)
1powB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 479;GLU 483 ASP 447;ASN 474;GLN 476(Magnesium binding)
1poxA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 479;GLU 483 ASP 447;ASN 474;GLN 476(Magnesium binding) mutant A458V
1poxB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 479;GLU 483 ASP 447;ASN 474;GLN 476(Magnesium binding) mutant A458V
1y9dA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 479;GLU 483 ASP 447;ASN 474;GLN 476(Magnesium binding)
1y9dB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 479;GLU 483 ASP 447;ASN 474;GLN 476(Magnesium binding)
1y9dC03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 479;GLU 483 ASP 447;ASN 474;GLN 476(Magnesium binding)
1y9dD03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain PHE 479;GLU 483 ASP 447;ASN 474;GLN 476(Magnesium binding)

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[3]
p.967
[4]
[5]
p.331-333
[8]
SCHEME 1, p.12933-12934
[10]
Scheme 1, Scheme 3, p.10754

References
[1]
Resource
Comments
Medline ID
PubMed ID 4896238
Journal Annu Rev Biochem
Year 1969
Volume 38
Pages 213-40
Authors Krampitz LO
Title Catalytic functions of thiamin diphosphate.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2037573
Journal J Biol Chem
Year 1991
Volume 266
Pages 10168-73
Authors Bertagnolli BL, Hager LP
Title Activation of Escherichia coli pyruvate oxidase enhances the oxidation of hydroxyethylthiamin pyrophosphate.
Related PDB
Related UniProtKB
[3]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS)
Medline ID 93174262
PubMed ID 8438155
Journal Science
Year 1993
Volume 259
Pages 965-7
Authors Muller YA, Schulz GE
Title Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase.
Related PDB
Related UniProtKB P37063
[4]
Resource
Comments
Medline ID
PubMed ID 8069629
Journal Structure
Year 1993
Volume 1
Pages 95-103
Authors Muller YA, Lindqvist Y, Furey W, Schulz GE, Jordan F, Schneider G
Title A thiamin diphosphate binding fold revealed by comparison of the crystal structures of transketolase, pyruvate oxidase and pyruvate decarboxylase.
Related PDB
Related UniProtKB
[5]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 AND 2.1 ANGSTROMS) OF WILD-TYPE AND MUTANT
Medline ID 94194507
PubMed ID 8145244
Journal J Mol Biol
Year 1994
Volume 237
Pages 315-35
Authors Muller YA, Schumacher G, Rudolph R, Schulz GE
Title The refined structures of a stabilized mutant and of wild-type pyruvate oxidase from Lactobacillus plantarum.
Related PDB 1pow 1pox
Related UniProtKB P37063
[6]
Resource
Comments
Medline ID
PubMed ID 9305946
Journal Biochemistry
Year 1997
Volume 36
Pages 11564-73
Authors Chang YY, Cronan JE Jr
Title Sulfhydryl chemistry detects three conformations of the lipid binding region of Escherichia coli pyruvate oxidase.
Related PDB
Related UniProtKB
[7]
Resource
Comments
Medline ID
PubMed ID 9655909
Journal Biochim Biophys Acta
Year 1998
Volume 1385
Pages 221-8
Authors Hubner G, Tittmann K, Killenberg-Jabs M, Schaffner J, Spinka M, Neef H, Kern D, Kern G, Schneider G, Wikner C, Ghisla S
Title Activation of thiamin diphosphate in enzymes.
Related PDB
Related UniProtKB
[8]
Resource
Comments
Medline ID
PubMed ID 9582325
Journal J Biol Chem
Year 1998
Volume 273
Pages 12929-34
Authors Tittmann K, Proske D, Spinka M, Ghisla S, Rudolph R, Hubner G, Kern G
Title Activation of thiamin diphosphate and FAD in the phosphatedependent pyruvate oxidase from Lactobacillus plantarum.
Related PDB
Related UniProtKB
[9]
Resource
Comments Review in a book; Academic Press Ltd., San Diego
Medline ID
PubMed ID
Journal Comprehensive Biological Catalysis (Editor: Sinnott M)
Year 1998
Volume
Pages 217-66
Authors Schowen RL
Title Thiamin-dependent Enzymes
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 10978159
Journal Biochemistry
Year 2000
Volume 39
Pages 10747-54
Authors Tittmann K, Golbik R, Ghisla S, Hubner G
Title Mechanism of elementary catalytic steps of pyruvate oxidase from Lactobacillus plantarum.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 10617618
Journal J Biol Chem
Year 2000
Volume 275
Pages 297-302
Authors Svergun DI, Petoukhov MV, Koch MH, Konig S
Title Crystal versus solution structures of thiamine diphosphate-dependent enzymes.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 11170450
Journal Biochemistry
Year 2001
Volume 40
Pages 1248-56
Authors Marchal D, Pantigny J, Laval JM, Moiroux J, Bourdillon C
Title Rate constants in two dimensions of electron transfer between pyruvate oxidase, a membrane enzyme, and ubiquinone (coenzyme Q8), its water-insoluble electron carrier.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 11514662
Journal Protein Sci
Year 2001
Volume 10
Pages 1712-28
Authors Dym O, Eisenberg D
Title Sequence-structure analysis of FAD-containing proteins.
Related PDB
Related UniProtKB
[14]
Resource
Comments
Medline ID
PubMed ID 15794646
Journal Biochemistry
Year 2005
Volume 44
Pages 5086-94
Authors Wille G, Ritter M, Weiss MS, Konig S, Mantele W, Hubner G
Title The role of Val-265 for flavin adenine dinucleotide (FAD) binding in pyruvate oxidase: FTIR, kinetic, and crystallographic studies on the enzyme variant V265A.
Related PDB 1y9d
Related UniProtKB

Comments
Although this enzyme binds magnesium ion, it is not involved in catalysis.
According to the literature [5], this enzyme catalyzes several reactions (Eq.1-Eq.4) as follwos:
(Eq.1) Pyruvate + ThDP-E-FAD(ox) = Oxyethyl-ThDP-E-FAD(ox) + CO2
(A) Addition of ThDP to Pyruvate
(B) Elimination of carboxylate (CO2), leading to Oxyethyl-ThDP Intermediate
(Eq.2) Oxyethyl-ThDP-E-FAD(ox) = Acetyl-ThDP-E-FAD(red)
(C) Hydride transfer from Oxyethyl-ThDP intermediate to FAD(ox)
(Eq.3) Acetyl-ThDP-E-FAD(red) + O2 = Acetyl-ThDP-E-FAD(ox) + H2O2
(D) Hydride transfer from FAD(red) to O2 (probably) Or oxygenation of FAD
(Eq.4) Acetyl-ThDP-E-FAD(ox) + Phosphate = Acetylphosphate + ThDP-E-FAD(ox)
(E) Phosphorolysis of Acetyl-ThDP intermediate

Created Updated
2004-03-24 2009-02-26