ID PDX2_ARATH Reviewed; 255 AA.
AC Q8LAD0; Q56ZP9; Q9FKJ3;
DT 09-JAN-2007, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2002, sequence version 1.
DT 27-MAR-2024, entry version 124.
DE RecName: Full=Probable pyridoxal 5'-phosphate synthase subunit PDX2;
DE Short=AtPDX2;
DE EC=4.3.3.6 {ECO:0000269|PubMed:17468224};
DE AltName: Full=Protein EMBRYO DEFECTIVE 2407;
DE AltName: Full=Pyridoxal 5'-phosphate synthase glutaminase subunit;
DE EC=3.5.1.2 {ECO:0000269|PubMed:17468224};
GN Name=PDX2; Synonyms=EMB2407; OrderedLocusNames=At5g60540;
GN ORFNames=muf9.190;
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9679202; DOI=10.1093/dnares/5.2.131;
RA Kaneko T., Kotani H., Nakamura Y., Sato S., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. V. Sequence
RT features of the regions of 1,381,565 bp covered by twenty one physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:131-145(1998).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=11910074; DOI=10.1126/science.1071006;
RA Seki M., Narusaka M., Kamiya A., Ishida J., Satou M., Sakurai T.,
RA Nakajima M., Enju A., Akiyama K., Oono Y., Muramatsu M., Hayashizaki Y.,
RA Kawai J., Carninci P., Itoh M., Ishii Y., Arakawa T., Shibata K.,
RA Shinagawa A., Shinozaki K.;
RT "Functional annotation of a full-length Arabidopsis cDNA collection.";
RL Science 296:141-145(2002).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RA Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B.,
RA Feldmann K.A.;
RT "Full-length cDNA from Arabidopsis thaliana.";
RL Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases.
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 211-255.
RC STRAIN=cv. Columbia;
RA Totoki Y., Seki M., Ishida J., Nakajima M., Enju A., Kamiya A.,
RA Narusaka M., Shin-i T., Nakagawa M., Sakamoto N., Oishi K., Kohara Y.,
RA Kobayashi M., Toyoda A., Sakaki Y., Sakurai T., Iida K., Akiyama K.,
RA Satou M., Toyoda T., Konagaya A., Carninci P., Kawai J., Hayashizaki Y.,
RA Shinozaki K.;
RT "Large-scale analysis of RIKEN Arabidopsis full-length (RAFL) cDNAs.";
RL Submitted (MAR-2005) to the EMBL/GenBank/DDBJ databases.
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, AND DISRUPTION PHENOTYPE.
RX PubMed=16157873; DOI=10.1073/pnas.0506228102;
RA Tambasco-Studart M., Titiz O., Raschle T., Forster G., Amrhein N.,
RA Fitzpatrick T.B.;
RT "Vitamin B6 biosynthesis in higher plants.";
RL Proc. Natl. Acad. Sci. U.S.A. 102:13687-13692(2005).
RN [8]
RP TISSUE SPECIFICITY, AND INTERACTION WITH PDX1.1 AND PDX1.3.
RC STRAIN=cv. C24;
RX PubMed=16766694; DOI=10.1105/tpc.105.036269;
RA Wagner S., Bernhardt A., Leuendorf J.E., Drewke C., Lytovchenko A.,
RA Mujahed N., Gurgui C., Frommer W.B., Leistner E., Fernie A.R., Hellmann H.;
RT "Analysis of the Arabidopsis rsr4-1/pdx1-3 mutant reveals the critical
RT function of the PDX1 protein family in metabolism, development, and vitamin
RT B6 biosynthesis.";
RL Plant Cell 18:1722-1735(2006).
RN [9]
RP FUNCTION, CATALYTIC ACTIVITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=17468224; DOI=10.1104/pp.107.096784;
RA Tambasco-Studart M., Tews I., Amrhein N., Fitzpatrick T.B.;
RT "Functional analysis of PDX2 from Arabidopsis, a glutaminase involved in
RT vitamin B6 biosynthesis.";
RL Plant Physiol. 144:915-925(2007).
RN [10]
RP INTERACTION WITH RPA2A.
RX PubMed=20706207; DOI=10.1038/msb.2010.53;
RA Van Leene J., Hollunder J., Eeckhout D., Persiau G., Van De Slijke E.,
RA Stals H., Van Isterdael G., Verkest A., Neirynck S., Buffel Y., De Bodt S.,
RA Maere S., Laukens K., Pharazyn A., Ferreira P.C.G., Eloy N., Renne C.,
RA Meyer C., Faure J.-D., Steinbrenner J., Beynon J., Larkin J.C.,
RA Van de Peer Y., Hilson P., Kuiper M., De Veylder L., Van Onckelen H.,
RA Inze D., Witters E., De Jaeger G.;
RT "Targeted interactomics reveals a complex core cell cycle machinery in
RT Arabidopsis thaliana.";
RL Mol. Syst. Biol. 6:397-397(2010).
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 PDX1.
CC Involved in the indirect resistance to singlet oxygen-generating
CC photosensitizers. {ECO:0000269|PubMed:16157873,
CC ECO:0000269|PubMed:17468224}.
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;
CC Evidence={ECO:0000269|PubMed:17468224};
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:0000269|PubMed:17468224};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.92 mM for L-glutamine {ECO:0000269|PubMed:16157873};
CC Note=kcat is 0.023 min(-1) for L-glutamine.
CC {ECO:0000269|PubMed:16157873};
CC -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC -!- SUBUNIT: Interacts with PDX1.1 or PDX1.3, but not with PDX1.2. Binds to
CC RPA2A. {ECO:0000269|PubMed:16766694, ECO:0000269|PubMed:20706207}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16157873}.
CC -!- TISSUE SPECIFICITY: Strongly expressed in roots, stems, leaves and
CC flowers. {ECO:0000269|PubMed:16766694}.
CC -!- DISRUPTION PHENOTYPE: Embryonic lethality when homozygous.
CC {ECO:0000269|PubMed:16157873}.
CC -!- MISCELLANEOUS: In plants, synthesis of vitamin B6 does not involve
CC deoxyxylulose 5-phosphate but utilizes intermediates from the pentose
CC phosphate pathway and from glycolysis.
CC -!- MISCELLANEOUS: Vitamin B6 is an essential quencher of singlet oxygen in
CC plants, that can protect cellular membranes from lipid peroxidation.
CC -!- SIMILARITY: Belongs to the glutaminase PdxT/SNO family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB08237.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC Sequence=BAD94363.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB011483; BAB08237.1; ALT_SEQ; Genomic_DNA.
DR EMBL; CP002688; AED97341.1; -; Genomic_DNA.
DR EMBL; AK117313; BAC41984.1; -; mRNA.
DR EMBL; BT005266; AAO63330.1; -; mRNA.
DR EMBL; AY087902; AAM65453.1; -; mRNA.
DR EMBL; AK220914; BAD94363.1; ALT_INIT; mRNA.
DR RefSeq; NP_568922.1; NM_125447.2.
DR AlphaFoldDB; Q8LAD0; -.
DR SMR; Q8LAD0; -.
DR BioGRID; 21419; 6.
DR IntAct; Q8LAD0; 5.
DR STRING; 3702.Q8LAD0; -.
DR MEROPS; C26.A32; -.
DR PaxDb; 3702-AT5G60540-1; -.
DR ProteomicsDB; 251262; -.
DR EnsemblPlants; AT5G60540.1; AT5G60540.1; AT5G60540.
DR GeneID; 836175; -.
DR Gramene; AT5G60540.1; AT5G60540.1; AT5G60540.
DR KEGG; ath:AT5G60540; -.
DR Araport; AT5G60540; -.
DR TAIR; AT5G60540; PDX2.
DR eggNOG; KOG3210; Eukaryota.
DR HOGENOM; CLU_069674_1_0_1; -.
DR InParanoid; Q8LAD0; -.
DR OMA; GMIMLAD; -.
DR OrthoDB; 842at2759; -.
DR PhylomeDB; Q8LAD0; -.
DR BioCyc; ARA:AT5G60540-MONOMER; -.
DR BioCyc; MetaCyc:AT5G60540-MONOMER; -.
DR UniPathway; UPA00245; -.
DR PRO; PR:Q8LAD0; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8LAD0; baseline and differential.
DR Genevisible; Q8LAD0; AT.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0004359; F:glutaminase activity; IDA:TAIR.
DR GO; GO:0046982; F:protein heterodimerization activity; IPI:TAIR.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
DR GO; GO:0006541; P:glutamine metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0042819; P:vitamin B6 biosynthetic process; IMP:TAIR.
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 NCBIfam; TIGR03800; PLP_synth_Pdx2; 1.
DR PANTHER; PTHR31559; PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT SNO; 1.
DR PANTHER; PTHR31559:SF0; PYRIDOXAL 5'-PHOSPHATE SYNTHASE SUBUNIT SNO1-RELATED; 1.
DR Pfam; PF01174; SNO; 1.
DR PIRSF; PIRSF005639; Glut_amidoT_SNO; 1.
DR SUPFAM; SSF52317; Class I glutamine amidotransferase-like; 1.
DR PROSITE; PS01236; PDXT_SNO_1; 1.
DR PROSITE; PS51130; PDXT_SNO_2; 1.
PE 1: Evidence at protein level;
KW Cytoplasm; Glutamine amidotransferase; Hydrolase; Lyase;
KW Pyridoxal phosphate; Reference proteome.
FT CHAIN 1..255
FT /note="Probable pyridoxal 5'-phosphate synthase subunit
FT PDX2"
FT /id="PRO_0000270626"
FT REGION 225..255
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 78
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT ACT_SITE 202
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT ACT_SITE 204
FT /note="Charge relay system"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT BINDING 46..48
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT BINDING 108
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT BINDING 142..143
FT /ligand="L-glutamine"
FT /ligand_id="ChEBI:CHEBI:58359"
FT /evidence="ECO:0000250|UniProtKB:P37528"
FT CONFLICT 212
FT /note="H -> P (in Ref. 6; BAD94363)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 255 AA; 27438 MW; 2B6447833990A677 CRC64;
MTVGVLALQG SFNEHIAALR RLGVQGVEIR KADQLLTVSS LIIPGGESTT MAKLAEYHNL
FPALREFVKM GKPVWGTCAG LIFLADRAVG QKEGGQELVG GLDCTVHRNF FGSQIQSFEA
DILVPQLTSQ EGGPETYRGV FIRAPAVLDV GPDVEVLADY PVPSNKVLYS SSTVQIQEED
ALPETKVIVA VKQGNLLATA FHPELTADTR WHSYFIKMTK EIEQGASSSS SKTIVSVGET
SAGPEPAKPD LPIFQ
//
