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Protein

Pyridoxal 5'-phosphate synthase subunit PdxT

Gene

pdxT

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

Functioni

Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The resulting ammonia molecule is channeled to the active site of PdxS.UniRule annotation1 Publication

Catalytic activityi

D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate.UniRule annotation1 Publication
L-glutamine + H2O = L-glutamate + NH3.UniRule annotation1 Publication

Kineticsi

kcat is 7.60 min(-1) for glutaminase activity.1 Publication

  1. KM=0.99 mM for L-glutamine1 Publication

    Pathwayi: pyridoxal 5'-phosphate biosynthesis

    This protein is involved in the pathway pyridoxal 5'-phosphate biosynthesis, which is part of Cofactor biosynthesis.UniRule annotation
    View all proteins of this organism that are known to be involved in the pathway pyridoxal 5'-phosphate biosynthesis and in Cofactor biosynthesis.

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei79 – 791NucleophileUniRule annotationCurated
    Binding sitei106 – 1061L-glutamineUniRule annotation1 Publication
    Active sitei170 – 1701Charge relay systemUniRule annotationCurated
    Active sitei172 – 1721Charge relay systemUniRule annotationCurated

    GO - Molecular functioni

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase, Lyase

    Keywords - Ligandi

    Pyridoxal phosphate

    Enzyme and pathway databases

    BioCyciBSUB:BSU00120-MONOMER.
    MetaCyc:MONOMER-15503.
    BRENDAi4.3.3.6. 658.
    UniPathwayiUPA00245.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Pyridoxal 5'-phosphate synthase subunit PdxTUniRule annotation (EC:4.3.3.6UniRule annotation1 Publication)
    Alternative name(s):
    Pdx2UniRule annotation
    Pyridoxal 5'-phosphate synthase glutaminase subunitUniRule annotation (EC:3.5.1.2UniRule annotation1 Publication)
    Gene namesi
    Name:pdxTUniRule annotation
    Synonyms:yaaE
    Ordered Locus Names:BSU00120
    OrganismiBacillus subtilis (strain 168)
    Taxonomic identifieri224308 [NCBI]
    Taxonomic lineageiBacteriaFirmicutesBacilliBacillalesBacillaceaeBacillus
    Proteomesi
    • UP000001570 Componenti: Chromosome

    Subcellular locationi

    GO - Cellular componenti

    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi10 – 101Q → A: 3-fold reduction in glutaminase activity. 1 Publication
    Mutagenesisi10 – 101Q → E: Almost no activity. 1 Publication
    Mutagenesisi10 – 101Q → N: 10-fold reduction in glutaminase activity. 1 Publication
    Mutagenesisi15 – 151E → A: Almost no effect on glutaminase activity. 1 Publication
    Mutagenesisi48 – 481E → A: No activity, disturbing interaction with PdxS. 1 Publication
    Mutagenesisi106 – 1061R → A: No activity, disturbing interaction with PdxS. 1 Publication
    Mutagenesisi135 – 1351R → A: No activity, disturbing interaction with PdxS. 1 Publication
    Mutagenesisi170 – 1701H → N: No activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 196196Pyridoxal 5'-phosphate synthase subunit PdxTPRO_0000135632Add
    BLAST

    Proteomic databases

    PaxDbiP37528.

    Interactioni

    Subunit structurei

    In the presence of PdxS, forms a dodecamer of heterodimers. Only shows activity in the heterodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    DIPiDIP-57719N.
    IntActiP37528. 1 interaction.
    MINTiMINT-7147884.
    STRINGi224308.Bsubs1_010100000060.

    Structurei

    Secondary structure

    1
    196
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 75Combined sources
    Beta strandi9 – 113Combined sources
    Helixi14 – 229Combined sources
    Beta strandi26 – 305Combined sources
    Helixi33 – 386Combined sources
    Beta strandi40 – 445Combined sources
    Helixi49 – 5810Combined sources
    Helixi62 – 709Combined sources
    Beta strandi75 – 784Combined sources
    Helixi80 – 856Combined sources
    Beta strandi86 – 894Combined sources
    Beta strandi102 – 1054Combined sources
    Turni106 – 1094Combined sources
    Turni111 – 1133Combined sources
    Beta strandi114 – 1207Combined sources
    Beta strandi129 – 1357Combined sources
    Beta strandi138 – 1425Combined sources
    Beta strandi147 – 1526Combined sources
    Beta strandi155 – 1617Combined sources
    Beta strandi164 – 1696Combined sources
    Beta strandi173 – 1753Combined sources
    Helixi178 – 19316Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1R9GX-ray2.50A/B1-196[»]
    2NV0X-ray1.73A/B1-196[»]
    2NV2X-ray2.12B/D/F/H/J/L/N/P/R/T/V/X1-196[»]
    ProteinModelPortaliP37528.
    SMRiP37528. Positions 1-196.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP37528.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni47 – 493L-glutamine bindingUniRule annotation1 Publication
    Regioni134 – 1352L-glutamine bindingUniRule annotation1 Publication

    Sequence similaritiesi

    Belongs to the glutaminase PdxT/SNO family.UniRule annotation

    Keywords - Domaini

    Glutamine amidotransferase

    Phylogenomic databases

    eggNOGiENOG4108UHX. Bacteria.
    COG0311. LUCA.
    HOGENOMiHOG000039949.
    InParanoidiP37528.
    KOiK08681.
    OMAiVYGTCAG.
    OrthoDBiEOG66F0BW.
    PhylomeDBiP37528.

    Family and domain databases

    Gene3Di3.40.50.880. 1 hit.
    HAMAPiMF_01615. PdxT.
    InterProiIPR029062. Class_I_gatase-like.
    IPR002161. PdxT/SNO.
    IPR021196. PdxT/SNO_CS.
    [Graphical view]
    PfamiPF01174. SNO. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005639. Glut_amidoT_SNO. 1 hit.
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR03800. PLP_synth_Pdx2. 1 hit.
    PROSITEiPS01236. PDXT_SNO_1. 1 hit.
    PS51130. PDXT_SNO_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P37528-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MLTIGVLGLQ GAVREHIHAI EACGAAGLVV KRPEQLNEVD GLILPGGEST
    60 70 80 90 100
    TMRRLIDTYQ FMEPLREFAA QGKPMFGTCA GLIILAKEIA GSDNPHLGLL
    110 120 130 140 150
    NVVVERNSFG RQVDSFEADL TIKGLDEPFT GVFIRAPHIL EAGENVEVLS
    160 170 180 190
    EHNGRIVAAK QGQFLGCSFH PELTEDHRVT QLFVEMVEEY KQKALV
    Length:196
    Mass (Da):21,447
    Last modified:October 1, 1994 - v1
    Checksum:i91111DEF75257882
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D26185 Genomic DNA. Translation: BAA05248.1.
    AL009126 Genomic DNA. Translation: CAB11788.1.
    PIRiS66042.
    RefSeqiNP_387893.1. NC_000964.3.
    WP_003226797.1. NZ_JNCM01000024.1.

    Genome annotation databases

    EnsemblBacteriaiCAB11788; CAB11788; BSU00120.
    GeneIDi939971.
    KEGGibsu:BSU00120.
    PATRICi18971483. VBIBacSub10457_0013.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    D26185 Genomic DNA. Translation: BAA05248.1.
    AL009126 Genomic DNA. Translation: CAB11788.1.
    PIRiS66042.
    RefSeqiNP_387893.1. NC_000964.3.
    WP_003226797.1. NZ_JNCM01000024.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1R9GX-ray2.50A/B1-196[»]
    2NV0X-ray1.73A/B1-196[»]
    2NV2X-ray2.12B/D/F/H/J/L/N/P/R/T/V/X1-196[»]
    ProteinModelPortaliP37528.
    SMRiP37528. Positions 1-196.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-57719N.
    IntActiP37528. 1 interaction.
    MINTiMINT-7147884.
    STRINGi224308.Bsubs1_010100000060.

    Proteomic databases

    PaxDbiP37528.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCAB11788; CAB11788; BSU00120.
    GeneIDi939971.
    KEGGibsu:BSU00120.
    PATRICi18971483. VBIBacSub10457_0013.

    Phylogenomic databases

    eggNOGiENOG4108UHX. Bacteria.
    COG0311. LUCA.
    HOGENOMiHOG000039949.
    InParanoidiP37528.
    KOiK08681.
    OMAiVYGTCAG.
    OrthoDBiEOG66F0BW.
    PhylomeDBiP37528.

    Enzyme and pathway databases

    UniPathwayiUPA00245.
    BioCyciBSUB:BSU00120-MONOMER.
    MetaCyc:MONOMER-15503.
    BRENDAi4.3.3.6. 658.

    Miscellaneous databases

    EvolutionaryTraceiP37528.

    Family and domain databases

    Gene3Di3.40.50.880. 1 hit.
    HAMAPiMF_01615. PdxT.
    InterProiIPR029062. Class_I_gatase-like.
    IPR002161. PdxT/SNO.
    IPR021196. PdxT/SNO_CS.
    [Graphical view]
    PfamiPF01174. SNO. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005639. Glut_amidoT_SNO. 1 hit.
    SUPFAMiSSF52317. SSF52317. 1 hit.
    TIGRFAMsiTIGR03800. PLP_synth_Pdx2. 1 hit.
    PROSITEiPS01236. PDXT_SNO_1. 1 hit.
    PS51130. PDXT_SNO_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Systematic sequencing of the 180 kilobase region of the Bacillus subtilis chromosome containing the replication origin."
      Ogasawara N., Nakai S., Yoshikawa H.
      DNA Res. 1:1-14(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: 168.
    2. "The complete genome sequence of the Gram-positive bacterium Bacillus subtilis."
      Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V., Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R., Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S., Bruschi C.V.
      , Caldwell B., Capuano V., Carter N.M., Choi S.-K., Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F., Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D., Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M., Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P., Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K., Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S., Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y., Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G., Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J., Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C., Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S., Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B., Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S., Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M., Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y., Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J., Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A., Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M., Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S., Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E., Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K., Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E., Yoshikawa H., Danchin A.
      Nature 390:249-256(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: 168.
    3. "On the two components of pyridoxal 5'-phosphate synthase from Bacillus subtilis."
      Raschle T., Amrhein N., Fitzpatrick T.B.
      J. Biol. Chem. 280:32291-32300(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 74-87, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, IDENTIFICATION OF REACTION PRODUCT, IDENTIFICATION OF ACTIVE SITE CYS.
      Strain: 168.
    4. "Physical and enzymological interaction of Bacillus subtilis proteins required for de novo pyridoxal 5'-phosphate biosynthesis."
      Belitsky B.R.
      J. Bacteriol. 186:1191-1196(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: CHARACTERIZATION.
      Strain: 168 / SMY.
    5. "Thermodynamic characterization of the protein-protein interaction in the heteromeric Bacillus subtilis pyridoxalphosphate synthase."
      Neuwirth M., Flicker K., Strohmeier M., Tews I., Macheroux P.
      Biochemistry 46:5131-5139(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: COMPLEX FORMATION OF PDXS AND PDXT.
    6. "Dissection of contributions from invariant amino acids to complex formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase complex from Bacillus subtilis."
      Wallner S., Neuwirth M., Flicker K., Tews I., Macheroux P.
      Biochemistry 48:1928-1935(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: MUTAGENESIS OF GLN-10; GLU-15; GLU-48; ARG-106 AND ARG-135.
    7. "Three-dimensional structure of YaaE from Bacillus subtilis, a glutaminase implicated in pyridoxal-5'-phosphate biosynthesis."
      Bauer J.A., Bennett E.M., Begley T.P., Ealick S.E.
      J. Biol. Chem. 279:2704-2711(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
    8. Cited for: X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF APOENZYME AND MUTANT ASN-170 IN COMPLEX WITH SUBUNIT PDXS AND GLUTAMINE, SUBUNIT, MUTAGENESIS OF HIS-170.
      Strain: 168 / CU1065.

    Entry informationi

    Entry nameiPDXT_BACSU
    AccessioniPrimary (citable) accession number: P37528
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: October 1, 1994
    Last modified: February 17, 2016
    This is version 114 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, Direct protein sequencing, 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
    5. Uncharacterized protein families (UPF)
      List of uncharacterized protein family (UPF) entries

    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.