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Protein

Glycine oxidase

Gene

thiO

Organism
Bacillus subtilis (strain 168)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the FAD-dependent oxidative deamination of various amines and D-amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Oxidizes sarcosine (N-methylglycine), N-ethylglycine and glycine (PubMed:9827558, PubMed:11744710, PubMed:19864430). Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine) (PubMed:19864430). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine (PubMed:9827558, PubMed:11744710). Does not act on L-amino acids and other D-amino acids (PubMed:9827558). Is essential for thiamine biosynthesis since the oxidation of glycine catalyzed by ThiO generates the glycine imine intermediate (dehydroglycine) required for the biosynthesis of the thiazole ring of thiamine pyrophosphate (PubMed:12627963).4 Publications

Catalytic activityi

Glycine + H2O + O2 = glyoxylate + NH3 + H2O2.3 Publications
N-ethylglycine + H2O + O2 = glyoxylate + ethylamine + H2O2.3 Publications
Sarcosine + H2O + O2 = glyoxylate + methylamine + H2O2.3 Publications
D-alanine + H2O + O2 = pyruvate + NH3 + H2O2.3 Publications
Glyphosate + H2O + O2 = glyoxylate + aminomethylphosphonate + H2O2.1 Publication

Cofactori

FAD1 PublicationNote: Binds 1 FAD per subunit.1 Publication

Enzyme regulationi

Is competitively inhibited by glycolate.1 Publication

Kineticsi

kcat is 1.3 sec(-1) with glycine as substrate. kcat is 1.6 sec(-1) with sarcosine as substrate. kcat is 1.4 sec(-1) with N-ethylglycine as substrate. kcat is 1.3 sec(-1) with D-proline as substrate. kcat is 1.1 sec(-1) with D-alanine as substrate (at pH 8.0) (PubMed:9827558). kcat is 0.60 sec(-1) with glycine as substrate. kcat is 0.91 sec(-1) with glyphosate as substrate (at pH 8.5 and 37 degrees Celsius) (PubMed:19864430).2 Publications
  1. KM=0.22 mM for sarcosine (at pH 8.0)1 Publication
  2. KM=0.66 mM for N-ethylglycine (at pH 8.0)1 Publication
  3. KM=0.99 mM for glycine (at pH 8.0)1 Publication
  4. KM=46 mM for D-proline (at pH 8.0)1 Publication
  5. KM=81 mM for D-alanine (at pH 8.0)1 Publication
  6. KM=0.7 mM for glycine (at pH 8.5 and 37 degrees Celsius)1 Publication
  7. KM=87 mM for glyphosate (at pH 8.5 and 37 degrees Celsius)1 Publication

    pH dependencei

    Optimum pH is 8.0.1 Publication

    Temperature dependencei

    Optimum temperature is 45 degrees Celsius.1 Publication

    Pathwayi: thiamine diphosphate biosynthesis

    This protein is involved in the pathway thiamine diphosphate biosynthesis, which is part of Cofactor biosynthesis.1 Publication
    View all proteins of this organism that are known to be involved in the pathway thiamine diphosphate biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei174FAD; via amide nitrogen and carbonyl oxygen3 Publications1
    Binding sitei302Substrate1 Publication1
    Binding sitei329Substrate1 Publication1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi14 – 15FAD3 Publications2
    Nucleotide bindingi34 – 35FAD3 Publications2
    Nucleotide bindingi42 – 43FAD3 Publications2
    Nucleotide bindingi47 – 49FAD3 Publications3
    Nucleotide bindingi327 – 333FAD3 Publications7

    GO - Molecular functioni

    • FAD binding Source: UniProtKB
    • glycine oxidase activity Source: UniProtKB
    • oxidoreductase activity Source: GO_Central

    GO - Biological processi

    • cellular amino acid metabolic process Source: UniProtKB
    • response to herbicide Source: UniProtKB-KW
    • thiamine biosynthetic process Source: UniProtKB
    • thiamine diphosphate biosynthetic process Source: UniProtKB-UniPathway

    Keywordsi

    Molecular functionOxidoreductase
    Biological processHerbicide resistance, Thiamine biosynthesis
    LigandFAD, Flavoprotein

    Enzyme and pathway databases

    BioCyciBSUB:BSU11670-MONOMER.
    MetaCyc:BSU11670-MONOMER.
    BRENDAi1.4.3.19. 658.
    SABIO-RKiO31616.
    UniPathwayiUPA00060.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycine oxidase2 Publications (EC:1.4.3.193 Publications)
    Short name:
    GO1 Publication
    Gene namesi
    Name:thiO1 Publication
    Synonyms:goxB1 Publication, yjbR1 Publication
    Ordered Locus Names:BSU11670
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Biotechnological usei

    Introducing the gene coding for the glycine oxidase mutant Ser-51/Arg-54/Ala-244 in plants may be an effective alternative mechanism for glyphosate tolerance in transgenic crops. In addition, transgenic plants that are able to oxidize glyphosate may represent an innovative bioremediation system for the soil treated with this herbicide.1 Publication

    Disruption phenotypei

    Cells lacking this gene have an absolute requirement for the thiazole alcohol for growth.1 Publication

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi51G → R: 130-fold decrease in catalytic efficiency on glycine and 28-fold increase in that on glyphosate. 1 Publication1
    Mutagenesisi51G → S: 60-fold decrease in catalytic efficiency on glycine and 210-fold increase in that on glyphosate; when associated with R-54 and A-244. 1 Publication1
    Mutagenesisi54A → R: 20-fold decrease in catalytic efficiency on glycine and 34-fold increase in that on glyphosate. 60-fold decrease in catalytic efficiency on glycine and 210-fold increase in that on glyphosate; when associated with S-51 and A-244. 1 Publication1
    Mutagenesisi244H → A: 2-fold decrease in catalytic efficiency on glycine and similar catalytic efficiency on glyphosate. 60-fold decrease in catalytic efficiency on glycine and 210-fold increase in that on glyphosate; when associated with S-51 and R-54. 1 Publication1

    Chemistry databases

    DrugBankiDB02713. Acetylamino-Acetic Acid.
    DB03147. Flavin adenine dinucleotide.
    DB03085. Hydroxyacetic Acid.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001627731 – 369Glycine oxidaseAdd BLAST369

    Proteomic databases

    PaxDbiO31616.

    Interactioni

    Subunit structurei

    Homotetramer.4 Publications

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100006451.

    Structurei

    Secondary structure

    1369
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi3 – 10Combined sources8
    Helixi14 – 25Combined sources12
    Beta strandi30 – 33Combined sources4
    Beta strandi35 – 37Combined sources3
    Turni38 – 41Combined sources4
    Helixi42 – 45Combined sources4
    Helixi52 – 54Combined sources3
    Helixi61 – 72Combined sources12
    Turni73 – 75Combined sources3
    Helixi76 – 84Combined sources9
    Beta strandi95 – 101Combined sources7
    Helixi102 – 109Combined sources8
    Turni110 – 113Combined sources4
    Beta strandi117 – 121Combined sources5
    Helixi122 – 128Combined sources7
    Beta strandi138 – 142Combined sources5
    Helixi150 – 163Combined sources14
    Beta strandi167 – 169Combined sources3
    Beta strandi176 – 178Combined sources3
    Beta strandi180 – 188Combined sources9
    Beta strandi191 – 200Combined sources10
    Helixi203 – 206Combined sources4
    Helixi207 – 212Combined sources6
    Beta strandi220 – 230Combined sources11
    Beta strandi232 – 234Combined sources3
    Beta strandi238 – 242Combined sources5
    Beta strandi245 – 249Combined sources5
    Beta strandi253 – 258Combined sources6
    Helixi272 – 285Combined sources14
    Helixi287 – 291Combined sources5
    Beta strandi292 – 304Combined sources13
    Beta strandi306 – 308Combined sources3
    Beta strandi311 – 315Combined sources5
    Beta strandi318 – 325Combined sources8
    Turni331 – 334Combined sources4
    Helixi335 – 346Combined sources12
    Helixi353 – 358Combined sources6

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1NG3X-ray2.60A/B1-369[»]
    1NG4X-ray2.30A/B1-369[»]
    1RYIX-ray1.80A/B/C/D1-367[»]
    3IF9X-ray2.60A/B/C/D1-369[»]
    ProteinModelPortaliO31616.
    SMRiO31616.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO31616.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DAO family. ThiO subfamily.Curated

    Phylogenomic databases

    eggNOGiCOG0665. LUCA.
    HOGENOMiHOG000042039.
    InParanoidiO31616.
    KOiK03153.
    OMAiVKGECLS.
    PhylomeDBiO31616.

    Family and domain databases

    Gene3Di3.50.50.60. 1 hit.
    InterProiView protein in InterPro
    IPR006076. FAD-dep_OxRdtase.
    IPR036188. FAD/NAD-bd_sf.
    IPR012727. Gly_oxidase_ThiO.
    PfamiView protein in Pfam
    PF01266. DAO. 1 hit.
    SUPFAMiSSF51905. SSF51905. 2 hits.
    TIGRFAMsiTIGR02352. thiamin_ThiO. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O31616-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKRHYEAVVI GGGIIGSAIA YYLAKENKNT ALFESGTMGG RTTSAAAGML
    60 70 80 90 100
    GAHAECEERD AFFDFAMHSQ RLYKGLGEEL YALSGVDIRQ HNGGMFKLAF
    110 120 130 140 150
    SEEDVLQLRQ MDDLDSVSWY SKEEVLEKEP YASGDIFGAS FIQDDVHVEP
    160 170 180 190 200
    YFVCKAYVKA AKMLGAEIFE HTPVLHVERD GEALFIKTPS GDVWANHVVV
    210 220 230 240 250
    ASGVWSGMFF KQLGLNNAFL PVKGECLSVW NDDIPLTKTL YHDHCYIVPR
    260 270 280 290 300
    KSGRLVVGAT MKPGDWSETP DLGGLESVMK KAKTMLPAIQ NMKVDRFWAG
    310 320 330 340 350
    LRPGTKDGKP YIGRHPEDSR ILFAAGHFRN GILLAPATGA LISDLIMNKE
    360
    VNQDWLHAFR IDRKEAVQI
    Length:369
    Mass (Da):40,937
    Last modified:January 1, 1998 - v1
    Checksum:i7A9466117AC0A76A
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL009126 Genomic DNA. Translation: CAB13024.1.
    PIRiB69845.
    RefSeqiNP_389049.1. NC_000964.3.
    WP_003245044.1. NZ_JNCM01000035.1.

    Genome annotation databases

    EnsemblBacteriaiCAB13024; CAB13024; BSU11670.
    GeneIDi939377.
    KEGGibsu:BSU11670.
    PATRICifig|224308.179.peg.1256.

    Similar proteinsi

    Entry informationi

    Entry nameiGLYOX_BACSU
    AccessioniPrimary (citable) accession number: O31616
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: January 1, 1998
    Last modified: October 25, 2017
    This is version 130 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Bacillus subtilis
      Bacillus subtilis (strain 168): entries, gene names and cross-references to SubtiList
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    4. SIMILARITY comments
      Index of protein domains and families