GLYOX_GEOKA
ID GLYOX_GEOKA Reviewed; 377 AA.
AC Q5L2C2;
DT 07-JUN-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-FEB-2005, sequence version 1.
DT 03-AUG-2022, entry version 91.
DE RecName: Full=Glycine oxidase {ECO:0000303|PubMed:17894345};
DE Short=GO;
DE Short=GOX {ECO:0000303|PubMed:17894345};
DE EC=1.4.3.19 {ECO:0000269|PubMed:17894345};
DE AltName: Full=GOXK {ECO:0000303|PubMed:17894345};
GN Name=thiO {ECO:0000250|UniProtKB:O31616};
GN OrderedLocusNames=GK0623 {ECO:0000312|EMBL:BAD74908.1};
OS Geobacillus kaustophilus (strain HTA426).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Geobacillus;
OC Geobacillus thermoleovorans group.
OX NCBI_TaxID=235909;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=HTA426;
RX PubMed=15576355; DOI=10.1093/nar/gkh970;
RA Takami H., Takaki Y., Chee G.-J., Nishi S., Shimamura S., Suzuki H.,
RA Matsui S., Uchiyama I.;
RT "Thermoadaptation trait revealed by the genome sequence of thermophilic
RT Geobacillus kaustophilus.";
RL Nucleic Acids Res. 32:6292-6303(2004).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBSTRATE
RP SPECIFICITY, COFACTOR, ACTIVITY REGULATION, SUBUNIT, 3D-STRUCTURE MODELING,
RP AND PATHWAY.
RC STRAIN=HTA426;
RX PubMed=17894345; DOI=10.1002/prot.21690;
RA Martinez-Martinez I., Navarro-Fernandez J., Garcia-Carmona F., Takami H.,
RA Sanchez-Ferrer A.;
RT "Characterization and structural modeling of a novel thermostable glycine
RT oxidase from Geobacillus kaustophilus HTA426.";
RL Proteins 70:1429-1441(2008).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS) IN COMPLEX WITH FAD AND GLYCINE, AND
RP COFACTOR.
RA Shiono T., Arai R., Nishiya Y., Nomura T.;
RT "Crystal structure of glycine oxidase from Geobacillus kaustophilus.";
RL Submitted (MAR-2015) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the FAD-dependent oxidative deamination of various
CC amines and D-amino acids to yield the corresponding alpha-keto acids,
CC ammonia/amine, and hydrogen peroxide. Oxidizes glycine, sarcosine (N-
CC methylglycine), N-ethylglycine, D-proline, D-alanine, glycine-ethyl
CC ester, and some other D-amino acids. Does not act on L-proline
CC (PubMed:17894345). Is essential for thiamine biosynthesis since the
CC oxidation of glycine catalyzed by ThiO generates the glycine imine
CC intermediate (dehydroglycine) required for the biosynthesis of the
CC thiazole ring of thiamine pyrophosphate (By similarity).
CC {ECO:0000250|UniProtKB:O31616, ECO:0000269|PubMed:17894345}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=glycine + H2O + O2 = glyoxylate + H2O2 + NH4(+);
CC Xref=Rhea:RHEA:11532, ChEBI:CHEBI:15377, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16240, ChEBI:CHEBI:28938, ChEBI:CHEBI:36655,
CC ChEBI:CHEBI:57305; EC=1.4.3.19;
CC Evidence={ECO:0000269|PubMed:17894345};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-ethylglycine + O2 = ethylamine + glyoxylate + H2O2;
CC Xref=Rhea:RHEA:12472, ChEBI:CHEBI:15377, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16240, ChEBI:CHEBI:36655, ChEBI:CHEBI:57440,
CC ChEBI:CHEBI:566789; EC=1.4.3.19;
CC Evidence={ECO:0000269|PubMed:17894345};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + O2 + sarcosine = glyoxylate + H2O2 + methylamine;
CC Xref=Rhea:RHEA:15165, ChEBI:CHEBI:15377, ChEBI:CHEBI:15379,
CC ChEBI:CHEBI:16240, ChEBI:CHEBI:36655, ChEBI:CHEBI:57433,
CC ChEBI:CHEBI:59338; EC=1.4.3.19;
CC Evidence={ECO:0000269|PubMed:17894345};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-alanine + H2O + O2 = H2O2 + NH4(+) + pyruvate;
CC Xref=Rhea:RHEA:22688, ChEBI:CHEBI:15361, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16240, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:57416; EC=1.4.3.19;
CC Evidence={ECO:0000269|PubMed:17894345};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:17894345, ECO:0000269|Ref.3};
CC Note=Binds 1 FAD per subunit. {ECO:0000269|Ref.3};
CC -!- ACTIVITY REGULATION: Is inhibited at high substrate concentration.
CC {ECO:0000269|PubMed:17894345}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.25 mM for glycine (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17894345};
CC KM=0.45 mM for sarcosine (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17894345};
CC KM=0.22 mM for N-ethylglycine (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17894345};
CC KM=9.30 mM for D-proline (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17894345};
CC KM=20.60 mM for D-alanine (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17894345};
CC KM=0.52 mM for glycine-ethyl ester (at pH 8.5 and 37 degrees Celsius)
CC {ECO:0000269|PubMed:17894345};
CC Note=Vmax with D-proline as substrate is 1.4-, 2.75-, 3.5- and 4.3-
CC fold higher than with glycine, sarcosine, D-alanine, and N-
CC ethylglycine, respectively. {ECO:0000269|PubMed:17894345};
CC pH dependence:
CC Optimum pH is 8.5. Is stable in the pH 6-9.5 range. A great decrease
CC in stability is only produced at pH values below pH 4.0.
CC {ECO:0000269|PubMed:17894345};
CC Temperature dependence:
CC Thermostable. Displays a Tm value of 2.5 hours at 60 degrees Celsius,
CC and 0.6 hour at 80 degrees Celsius. {ECO:0000269|PubMed:17894345};
CC -!- PATHWAY: Cofactor biosynthesis; thiamine diphosphate biosynthesis.
CC {ECO:0000250|UniProtKB:O31616, ECO:0000305|PubMed:17894345}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000269|PubMed:17894345}.
CC -!- SIMILARITY: Belongs to the DAO family. ThiO subfamily. {ECO:0000305}.
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DR EMBL; BA000043; BAD74908.1; -; Genomic_DNA.
DR RefSeq; WP_011230127.1; NC_006510.1.
DR PDB; 4YSH; X-ray; 2.20 A; A/B=1-377.
DR PDBsum; 4YSH; -.
DR AlphaFoldDB; Q5L2C2; -.
DR SMR; Q5L2C2; -.
DR STRING; 235909.GK0623; -.
DR EnsemblBacteria; BAD74908; BAD74908; GK0623.
DR KEGG; gka:GK0623; -.
DR eggNOG; COG0665; Bacteria.
DR HOGENOM; CLU_007884_4_5_9; -.
DR OMA; GCGTLWL; -.
DR BRENDA; 1.4.3.19; 8138.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000001172; Chromosome.
DR GO; GO:0071949; F:FAD binding; IDA:UniProtKB.
DR GO; GO:0043799; F:glycine oxidase activity; IDA:UniProtKB.
DR GO; GO:0006520; P:cellular amino acid metabolic process; IDA:UniProtKB.
DR GO; GO:0051289; P:protein homotetramerization; IDA:UniProtKB.
DR GO; GO:0009228; P:thiamine biosynthetic process; IEA:UniProtKB-KW.
DR GO; GO:0009229; P:thiamine diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR006076; FAD-dep_OxRdtase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR012727; Gly_oxidase_ThiO.
DR Pfam; PF01266; DAO; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
DR TIGRFAMs; TIGR02352; thiamin_ThiO; 1.
PE 1: Evidence at protein level;
KW 3D-structure; FAD; Flavoprotein; Oxidoreductase; Reference proteome;
KW Thiamine biosynthesis.
FT CHAIN 1..377
FT /note="Glycine oxidase"
FT /id="PRO_0000440180"
FT BINDING 14..15
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 34..35
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 42..43
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 47..49
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 180
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 309
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 334..340
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 336
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.3"
FT STRAND 4..10
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 14..25
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 30..33
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:4YSH"
FT TURN 38..41
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 42..45
FT /evidence="ECO:0007829|PDB:4YSH"
FT TURN 52..54
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 62..84
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 95..99
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 102..112
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 114..117
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 123..125
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 129..132
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 142..148
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 156..169
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 180..184
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 187..194
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 197..206
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 209..211
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 212..217
FT /evidence="ECO:0007829|PDB:4YSH"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 225..236
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 243..251
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 253..257
FT /evidence="ECO:0007829|PDB:4YSH"
FT TURN 258..260
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 261..265
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 279..292
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 294..298
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 299..312
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 318..321
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 323..325
FT /evidence="ECO:0007829|PDB:4YSH"
FT STRAND 328..332
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 338..353
FT /evidence="ECO:0007829|PDB:4YSH"
FT HELIX 363..365
FT /evidence="ECO:0007829|PDB:4YSH"
SQ SEQUENCE 377 AA; 39913 MW; DE840B80243B9929 CRC64;
MTHRYDVAIV GGGVIGAAIG FELAKRRHRV AIFEKGTMGS GASSAAAGML GAQSEFSTSS
PLVPLALQSR ALMPALAEEL RERTGIDIGL VEKGLIKLAT TEEEADDLYR HYTFWRGIGE
PVQWLTKGEA LEMEPRLAAE ALAGAMYIPG DGQVSAPDLA AALAYAAASA GACLYEYTEV
FDIRSDSSGH VLDTTGGTFA AEAVVIASGA WAARLGARVG LSLSVYPVKG ECVMVRAPVP
LLQTTVFAKN GCYIVPKSGN RLLIGATSTP GTFDRRVSAG GVMNLLHRAA HLVPDIEQAE
WVASWSGIRP QTEDGLPYLG EHPERRGLFV AAGHYRNGIL LSPLTGLLVA DLVERKETAF
DLAPFSLTRH IGKVGVE
