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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. Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine. Does not act on L-amino acids and other D-amino acids. 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.2 Publications

Catalytic activityi

Glycine + H2O + O2 = glyoxylate + NH3 + H2O2.2 Publications

Cofactori

FADNote: Binds 1 FAD per subunit.

Kineticsi

  1. KM=0.22 mM for sarcosine (at pH 8)2 Publications
  2. KM=0.66 mM for N-ethylglycine (at pH 8)2 Publications
  3. KM=0.99 mM for glycine (at pH 8)2 Publications
  4. KM=46 mM for D-proline (at pH 8)2 Publications
  5. KM=81 mM for D-alanine (at pH 8)2 Publications
  6. KM=87 mM for glyphosate2 Publications

    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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei55 – 551Substrate
    Binding sitei174 – 1741FAD; via amide nitrogen and carbonyl oxygen2 Publications
    Binding sitei302 – 3021Substrate
    Binding sitei329 – 3291Substrate

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi7 – 2115FAD2 PublicationsAdd
    BLAST
    Nucleotide bindingi34 – 352FAD2 Publications
    Nucleotide bindingi42 – 432FAD2 Publications
    Nucleotide bindingi47 – 493FAD2 Publications
    Nucleotide bindingi327 – 3337FAD2 Publications

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Oxidoreductase

    Keywords - Biological processi

    Herbicide resistance, Thiamine biosynthesis

    Keywords - Ligandi

    FAD, Flavoprotein

    Enzyme and pathway databases

    BioCyciBSUB:BSU11670-MONOMER.
    MetaCyc:BSU11670-MONOMER.
    BRENDAi1.4.3.19. 658.
    SABIO-RKO31616.
    UniPathwayiUPA00060.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Glycine oxidase (EC:1.4.3.19)
    Short name:
    GO
    Gene namesi
    Name:thiO
    Synonyms:goxB, yjbR
    Ordered Locus Names:BSU11670
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    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 is 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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi51 – 511G → R: 130-fold decrease in catalytic efficiency on glycine and 28-fold increase in that on glyphosate. 1 Publication
    Mutagenesisi51 – 511G → 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 Publication
    Mutagenesisi54 – 541A → 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 Publication
    Mutagenesisi244 – 2441H → 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 Publication

    Chemistry

    DrugBankiDB03147. Flavin adenine dinucleotide.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 369369Glycine oxidasePRO_0000162773Add
    BLAST

    Proteomic databases

    PaxDbiO31616.

    Interactioni

    Subunit structurei

    Homotetramer.4 Publications

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100006451.

    Structurei

    Secondary structure

    1
    369
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 108Combined sources
    Helixi14 – 2512Combined sources
    Beta strandi30 – 334Combined sources
    Beta strandi35 – 373Combined sources
    Turni38 – 414Combined sources
    Helixi42 – 454Combined sources
    Helixi52 – 543Combined sources
    Helixi61 – 7212Combined sources
    Turni73 – 753Combined sources
    Helixi76 – 849Combined sources
    Beta strandi95 – 1017Combined sources
    Helixi102 – 1098Combined sources
    Turni110 – 1134Combined sources
    Beta strandi117 – 1215Combined sources
    Helixi122 – 1287Combined sources
    Beta strandi138 – 1425Combined sources
    Helixi150 – 16314Combined sources
    Beta strandi167 – 1693Combined sources
    Beta strandi176 – 1783Combined sources
    Beta strandi180 – 1889Combined sources
    Beta strandi191 – 20010Combined sources
    Helixi203 – 2064Combined sources
    Helixi207 – 2126Combined sources
    Beta strandi220 – 23011Combined sources
    Beta strandi232 – 2343Combined sources
    Beta strandi238 – 2425Combined sources
    Beta strandi245 – 2495Combined sources
    Beta strandi253 – 2586Combined sources
    Helixi272 – 28514Combined sources
    Helixi287 – 2915Combined sources
    Beta strandi292 – 30413Combined sources
    Beta strandi306 – 3083Combined sources
    Beta strandi311 – 3155Combined sources
    Beta strandi318 – 3258Combined sources
    Turni331 – 3344Combined sources
    Helixi335 – 34612Combined sources
    Helixi353 – 3586Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-364.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO31616.

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the DAO family.Curated

    Phylogenomic databases

    eggNOGiCOG0665. LUCA.
    HOGENOMiHOG000042039.
    InParanoidiO31616.
    KOiK03153.
    OMAiCTPDLKP.
    PhylomeDBiO31616.

    Family and domain databases

    Gene3Di3.50.50.60. 3 hits.
    InterProiIPR006076. FAD-dep_OxRdtase.
    IPR023753. FAD/NAD-binding_dom.
    IPR012727. Gly_oxidase_ThiO.
    [Graphical view]
    PfamiPF01266. DAO. 1 hit.
    [Graphical view]
    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.
    PATRICi18974051. VBIBacSub10457_1219.

    Cross-referencesi

    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.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    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. Positions 1-364.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi224308.Bsubs1_010100006451.

    Chemistry

    DrugBankiDB03147. Flavin adenine dinucleotide.

    Proteomic databases

    PaxDbiO31616.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB13024; CAB13024; BSU11670.
    GeneIDi939377.
    KEGGibsu:BSU11670.
    PATRICi18974051. VBIBacSub10457_1219.

    Phylogenomic databases

    eggNOGiCOG0665. LUCA.
    HOGENOMiHOG000042039.
    InParanoidiO31616.
    KOiK03153.
    OMAiCTPDLKP.
    PhylomeDBiO31616.

    Enzyme and pathway databases

    UniPathwayiUPA00060.
    BioCyciBSUB:BSU11670-MONOMER.
    MetaCyc:BSU11670-MONOMER.
    BRENDAi1.4.3.19. 658.
    SABIO-RKO31616.

    Miscellaneous databases

    EvolutionaryTraceiO31616.

    Family and domain databases

    Gene3Di3.50.50.60. 3 hits.
    InterProiIPR006076. FAD-dep_OxRdtase.
    IPR023753. FAD/NAD-binding_dom.
    IPR012727. Gly_oxidase_ThiO.
    [Graphical view]
    PfamiPF01266. DAO. 1 hit.
    [Graphical view]
    SUPFAMiSSF51905. SSF51905. 2 hits.
    TIGRFAMsiTIGR02352. thiamin_ThiO. 1 hit.
    ProtoNetiSearch...

    Entry informationi

    Entry nameiGLOX_BACSU
    AccessioniPrimary (citable) accession number: O31616
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 15, 1998
    Last sequence update: January 1, 1998
    Last modified: September 7, 2016
    This is version 122 of the entry and version 1 of the sequence. [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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.