PDXT_BACSU
ID PDXT_BACSU Reviewed; 196 AA.
AC P37528;
DT 01-OCT-1994, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-1994, sequence version 1.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Pyridoxal 5'-phosphate synthase subunit PdxT {ECO:0000255|HAMAP-Rule:MF_01615};
DE EC=4.3.3.6 {ECO:0000255|HAMAP-Rule:MF_01615, ECO:0000269|PubMed:16030023};
DE AltName: Full=Pdx2 {ECO:0000255|HAMAP-Rule:MF_01615};
DE AltName: Full=Pyridoxal 5'-phosphate synthase glutaminase subunit {ECO:0000255|HAMAP-Rule:MF_01615};
DE EC=3.5.1.2 {ECO:0000255|HAMAP-Rule:MF_01615, ECO:0000269|PubMed:16030023};
GN Name=pdxT {ECO:0000255|HAMAP-Rule:MF_01615}; Synonyms=yaaE;
GN OrderedLocusNames=BSU00120;
OS Bacillus subtilis (strain 168).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus.
OX NCBI_TaxID=224308;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=168;
RX PubMed=7584024; DOI=10.1093/dnares/1.1.1;
RA Ogasawara N., Nakai S., Yoshikawa H.;
RT "Systematic sequencing of the 180 kilobase region of the Bacillus subtilis
RT chromosome containing the replication origin.";
RL DNA Res. 1:1-14(1994).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=168;
RX PubMed=9384377; DOI=10.1038/36786;
RA Kunst F., Ogasawara N., Moszer I., Albertini A.M., Alloni G., Azevedo V.,
RA Bertero M.G., Bessieres P., Bolotin A., Borchert S., Borriss R.,
RA Boursier L., Brans A., Braun M., Brignell S.C., Bron S., Brouillet S.,
RA Bruschi C.V., Caldwell B., Capuano V., Carter N.M., Choi S.-K.,
RA Codani J.-J., Connerton I.F., Cummings N.J., Daniel R.A., Denizot F.,
RA Devine K.M., Duesterhoeft A., Ehrlich S.D., Emmerson P.T., Entian K.-D.,
RA Errington J., Fabret C., Ferrari E., Foulger D., Fritz C., Fujita M.,
RA Fujita Y., Fuma S., Galizzi A., Galleron N., Ghim S.-Y., Glaser P.,
RA Goffeau A., Golightly E.J., Grandi G., Guiseppi G., Guy B.J., Haga K.,
RA Haiech J., Harwood C.R., Henaut A., Hilbert H., Holsappel S., Hosono S.,
RA Hullo M.-F., Itaya M., Jones L.-M., Joris B., Karamata D., Kasahara Y.,
RA Klaerr-Blanchard M., Klein C., Kobayashi Y., Koetter P., Koningstein G.,
RA Krogh S., Kumano M., Kurita K., Lapidus A., Lardinois S., Lauber J.,
RA Lazarevic V., Lee S.-M., Levine A., Liu H., Masuda S., Mauel C.,
RA Medigue C., Medina N., Mellado R.P., Mizuno M., Moestl D., Nakai S.,
RA Noback M., Noone D., O'Reilly M., Ogawa K., Ogiwara A., Oudega B.,
RA Park S.-H., Parro V., Pohl T.M., Portetelle D., Porwollik S.,
RA Prescott A.M., Presecan E., Pujic P., Purnelle B., Rapoport G., Rey M.,
RA Reynolds S., Rieger M., Rivolta C., Rocha E., Roche B., Rose M., Sadaie Y.,
RA Sato T., Scanlan E., Schleich S., Schroeter R., Scoffone F., Sekiguchi J.,
RA Sekowska A., Seror S.J., Serror P., Shin B.-S., Soldo B., Sorokin A.,
RA Tacconi E., Takagi T., Takahashi H., Takemaru K., Takeuchi M.,
RA Tamakoshi A., Tanaka T., Terpstra P., Tognoni A., Tosato V., Uchiyama S.,
RA Vandenbol M., Vannier F., Vassarotti A., Viari A., Wambutt R., Wedler E.,
RA Wedler H., Weitzenegger T., Winters P., Wipat A., Yamamoto H., Yamane K.,
RA Yasumoto K., Yata K., Yoshida K., Yoshikawa H.-F., Zumstein E.,
RA Yoshikawa H., Danchin A.;
RT "The complete genome sequence of the Gram-positive bacterium Bacillus
RT subtilis.";
RL Nature 390:249-256(1997).
RN [3]
RP PROTEIN SEQUENCE OF 74-87, FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL
RP PROPERTIES, IDENTIFICATION OF REACTION PRODUCT, AND IDENTIFICATION OF
RP ACTIVE SITE CYS.
RC STRAIN=168;
RX PubMed=16030023; DOI=10.1074/jbc.m501356200;
RA Raschle T., Amrhein N., Fitzpatrick T.B.;
RT "On the two components of pyridoxal 5'-phosphate synthase from Bacillus
RT subtilis.";
RL J. Biol. Chem. 280:32291-32300(2005).
RN [4]
RP CHARACTERIZATION.
RC STRAIN=168 / SMY;
RX PubMed=14762015; DOI=10.1128/jb.186.4.1191-1196.2004;
RA Belitsky B.R.;
RT "Physical and enzymological interaction of Bacillus subtilis proteins
RT required for de novo pyridoxal 5'-phosphate biosynthesis.";
RL J. Bacteriol. 186:1191-1196(2004).
RN [5]
RP COMPLEX FORMATION OF PDXS AND PDXT.
RX PubMed=17408246; DOI=10.1021/bi602602x;
RA Neuwirth M., Flicker K., Strohmeier M., Tews I., Macheroux P.;
RT "Thermodynamic characterization of the protein-protein interaction in the
RT heteromeric Bacillus subtilis pyridoxalphosphate synthase.";
RL Biochemistry 46:5131-5139(2007).
RN [6]
RP MUTAGENESIS OF GLN-10; GLU-15; GLU-48; ARG-106 AND ARG-135.
RX PubMed=19152323; DOI=10.1021/bi801887r;
RA Wallner S., Neuwirth M., Flicker K., Tews I., Macheroux P.;
RT "Dissection of contributions from invariant amino acids to complex
RT formation and catalysis in the heteromeric pyridoxal 5-phosphate synthase
RT complex from Bacillus subtilis.";
RL Biochemistry 48:1928-1935(2009).
RN [7]
RP X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
RX PubMed=14585832; DOI=10.1074/jbc.m310311200;
RA Bauer J.A., Bennett E.M., Begley T.P., Ealick S.E.;
RT "Three-dimensional structure of YaaE from Bacillus subtilis, a glutaminase
RT implicated in pyridoxal-5'-phosphate biosynthesis.";
RL J. Biol. Chem. 279:2704-2711(2004).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.73 ANGSTROMS) OF APOENZYME AND MUTANT ASN-170 IN
RP COMPLEX WITH SUBUNIT PDXS AND GLUTAMINE, SUBUNIT, AND MUTAGENESIS OF
RP HIS-170.
RC STRAIN=168 / CU1065;
RX PubMed=17159152; DOI=10.1073/pnas.0604950103;
RA Strohmeier M., Raschle T., Mazurkiewicz J., Rippe K., Sinning I.,
RA Fitzpatrick T.B., Tews I.;
RT "Structure of a bacterial pyridoxal 5'-phosphate synthase complex.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:19284-19289(2006).
CC -!- FUNCTION: Catalyzes the hydrolysis of glutamine to glutamate and
CC ammonia as part of the biosynthesis of pyridoxal 5'-phosphate. The
CC resulting ammonia molecule is channeled to the active site of PdxS.
CC {ECO:0000255|HAMAP-Rule:MF_01615, ECO:0000269|PubMed:16030023}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=aldehydo-D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate +
CC L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate + pyridoxal 5'-
CC phosphate; Xref=Rhea:RHEA:31507, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58273, ChEBI:CHEBI:58359, ChEBI:CHEBI:59776,
CC ChEBI:CHEBI:597326; EC=4.3.3.6; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01615, ECO:0000269|PubMed:16030023};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L-glutamine = L-glutamate + NH4(+);
CC Xref=Rhea:RHEA:15889, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:58359; EC=3.5.1.2;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01615,
CC ECO:0000269|PubMed:16030023};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=0.99 mM for L-glutamine {ECO:0000269|PubMed:16030023};
CC Note=kcat is 7.60 min(-1) for glutaminase activity.
CC {ECO:0000269|PubMed:16030023};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_01615}.
CC -!- SUBUNIT: In the presence of PdxS, forms a dodecamer of heterodimers.
CC Only shows activity in the heterodimer. {ECO:0000255|HAMAP-
CC Rule:MF_01615, ECO:0000269|PubMed:17159152}.
CC -!- INTERACTION:
CC P37528; P37527: pdxS; NbExp=5; IntAct=EBI-7051766, EBI-7828661;
CC P37528; P37528: pdxT; NbExp=2; IntAct=EBI-7051766, EBI-7051766;
CC -!- SIMILARITY: Belongs to the glutaminase PdxT/SNO family.
CC {ECO:0000255|HAMAP-Rule:MF_01615}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; D26185; BAA05248.1; -; Genomic_DNA.
DR EMBL; AL009126; CAB11788.1; -; Genomic_DNA.
DR PIR; S66042; S66042.
DR RefSeq; NP_387893.1; NC_000964.3.
DR RefSeq; WP_003226797.1; NZ_JNCM01000024.1.
DR PDB; 1R9G; X-ray; 2.50 A; A/B=1-196.
DR PDB; 2NV0; X-ray; 1.73 A; A/B=1-196.
DR PDB; 2NV2; X-ray; 2.12 A; B/D/F/H/J/L/N/P/R/T/V/X=1-196.
DR PDBsum; 1R9G; -.
DR PDBsum; 2NV0; -.
DR PDBsum; 2NV2; -.
DR AlphaFoldDB; P37528; -.
DR SMR; P37528; -.
DR DIP; DIP-57719N; -.
DR IntAct; P37528; 2.
DR MINT; P37528; -.
DR STRING; 224308.BSU00120; -.
DR PaxDb; P37528; -.
DR PRIDE; P37528; -.
DR EnsemblBacteria; CAB11788; CAB11788; BSU_00120.
DR GeneID; 939971; -.
DR KEGG; bsu:BSU00120; -.
DR PATRIC; fig|224308.179.peg.12; -.
DR eggNOG; COG0311; Bacteria.
DR InParanoid; P37528; -.
DR OMA; VFIRAPI; -.
DR PhylomeDB; P37528; -.
DR BioCyc; BSUB:BSU00120-MON; -.
DR BioCyc; MetaCyc:MON-15503; -.
DR BRENDA; 4.3.3.6; 658.
DR SABIO-RK; P37528; -.
DR UniPathway; UPA00245; -.
DR EvolutionaryTrace; P37528; -.
DR Proteomes; UP000001570; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:1903600; C:glutaminase complex; IBA:GO_Central.
DR GO; GO:0004359; F:glutaminase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0006543; P:glutamine catabolic process; IEA:UniProtKB-UniRule.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008614; P:pyridoxine metabolic process; IBA:GO_Central.
DR CDD; cd01749; GATase1_PB; 1.
DR Gene3D; 3.40.50.880; -; 1.
DR HAMAP; MF_01615; PdxT; 1.
DR InterPro; IPR029062; Class_I_gatase-like.
DR InterPro; IPR002161; PdxT/SNO.
DR InterPro; IPR021196; PdxT/SNO_CS.
DR PANTHER; PTHR31559; PTHR31559; 1.
DR Pfam; PF01174; SNO; 1.
DR PIRSF; PIRSF005639; Glut_amidoT_SNO; 1.
DR SUPFAM; SSF52317; SSF52317; 1.
DR TIGRFAMs; TIGR03800; PLP_synth_Pdx2; 1.
DR PROSITE; PS01236; PDXT_SNO_1; 1.
DR PROSITE; PS51130; PDXT_SNO_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Glutamine amidotransferase;
KW Hydrolase; Lyase; Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..196
FT /note="Pyridoxal 5'-phosphate synthase subunit PdxT"
FT /id="PRO_0000135632"
FT ACT_SITE 79
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01615, ECO:0000305"
FT ACT_SITE 170
FT /note="Charge relay system"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01615, ECO:0000305"
FT ACT_SITE 172
FT /note="Charge relay system"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01615, ECO:0000305"
FT BINDING 47..49
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01615,
FT ECO:0000269|PubMed:17159152"
FT BINDING 106
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01615,
FT ECO:0000269|PubMed:17159152"
FT BINDING 134..135
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01615,
FT ECO:0000269|PubMed:17159152"
FT MUTAGEN 10
FT /note="Q->A: 3-fold reduction in glutaminase activity."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 10
FT /note="Q->E: Almost no activity."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 10
FT /note="Q->N: 10-fold reduction in glutaminase activity."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 15
FT /note="E->A: Almost no effect on glutaminase activity."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 48
FT /note="E->A: No activity, disturbing interaction with
FT PdxS."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 106
FT /note="R->A: No activity, disturbing interaction with
FT PdxS."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 135
FT /note="R->A: No activity, disturbing interaction with
FT PdxS."
FT /evidence="ECO:0000269|PubMed:19152323"
FT MUTAGEN 170
FT /note="H->N: No activity."
FT /evidence="ECO:0000269|PubMed:17159152"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 9..11
FT /evidence="ECO:0007829|PDB:2NV0"
FT HELIX 14..22
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 26..30
FT /evidence="ECO:0007829|PDB:2NV0"
FT HELIX 33..38
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 40..44
FT /evidence="ECO:0007829|PDB:2NV0"
FT HELIX 49..58
FT /evidence="ECO:0007829|PDB:2NV0"
FT HELIX 62..70
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 75..78
FT /evidence="ECO:0007829|PDB:2NV0"
FT HELIX 80..85
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:2NV2"
FT STRAND 102..105
FT /evidence="ECO:0007829|PDB:2NV0"
FT TURN 106..109
FT /evidence="ECO:0007829|PDB:2NV2"
FT TURN 111..113
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 114..120
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 129..135
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 138..142
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 147..152
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 155..161
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 164..169
FT /evidence="ECO:0007829|PDB:2NV0"
FT STRAND 173..175
FT /evidence="ECO:0007829|PDB:2NV0"
FT HELIX 178..193
FT /evidence="ECO:0007829|PDB:2NV0"
SQ SEQUENCE 196 AA; 21447 MW; 91111DEF75257882 CRC64;
MLTIGVLGLQ GAVREHIHAI EACGAAGLVV KRPEQLNEVD GLILPGGEST TMRRLIDTYQ
FMEPLREFAA QGKPMFGTCA GLIILAKEIA GSDNPHLGLL NVVVERNSFG RQVDSFEADL
TIKGLDEPFT GVFIRAPHIL EAGENVEVLS EHNGRIVAAK QGQFLGCSFH PELTEDHRVT
QLFVEMVEEY KQKALV
