PDX13_ARATH
ID PDX13_ARATH Reviewed; 309 AA.
AC Q8L940; Q3KRU4; Q9M032;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2004, sequence version 2.
DT 03-AUG-2022, entry version 147.
DE RecName: Full=Pyridoxal 5'-phosphate synthase subunit PDX1.3;
DE Short=AtPDX1.3;
DE Short=AtPDX1;1;
DE Short=PLP synthase subunit PDX1.3;
DE EC=4.3.3.6 {ECO:0000269|PubMed:17468224};
GN Name=PDX13; Synonyms=GIP2, PDX1L3, RSR4; OrderedLocusNames=At5g01410;
GN ORFNames=T10O8.120;
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 FUNCTION, TISSUE SPECIFICITY, INDUCTION, SUBCELLULAR LOCATION, AND
RP DISRUPTION PHENOTYPE.
RX PubMed=16236150; DOI=10.1111/j.1365-313x.2005.02538.x;
RA Chen H., Xiong L.;
RT "Pyridoxine is required for post-embryonic root development and tolerance
RT to osmotic and oxidative stresses.";
RL Plant J. 44:396-408(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], MUTAGENESIS OF GLY-54, TISSUE
RP SPECIFICITY, AND INTERACTION WITH PDX1.1; PDX1.2 AND PDX2.
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 [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=11130714; DOI=10.1038/35048507;
RA Tabata S., Kaneko T., Nakamura Y., Kotani H., Kato T., Asamizu E.,
RA Miyajima N., Sasamoto S., Kimura T., Hosouchi T., Kawashima K., Kohara M.,
RA Matsumoto M., Matsuno A., Muraki A., Nakayama S., Nakazaki N., Naruo K.,
RA Okumura S., Shinpo S., Takeuchi C., Wada T., Watanabe A., Yamada M.,
RA Yasuda M., Sato S., de la Bastide M., Huang E., Spiegel L., Gnoj L.,
RA O'Shaughnessy A., Preston R., Habermann K., Murray J., Johnson D.,
RA Rohlfing T., Nelson J., Stoneking T., Pepin K., Spieth J., Sekhon M.,
RA Armstrong J., Becker M., Belter E., Cordum H., Cordes M., Courtney L.,
RA Courtney W., Dante M., Du H., Edwards J., Fryman J., Haakensen B.,
RA Lamar E., Latreille P., Leonard S., Meyer R., Mulvaney E., Ozersky P.,
RA Riley A., Strowmatt C., Wagner-McPherson C., Wollam A., Yoakum M., Bell M.,
RA Dedhia N., Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D.,
RA Baker J., Kirchoff K., Toth K., King L., Bahret A., Miller B., Marra M.A.,
RA Martienssen R., McCombie W.R., Wilson R.K., Murphy G., Bancroft I.,
RA Volckaert G., Wambutt R., Duesterhoeft A., Stiekema W., Pohl T.,
RA Entian K.-D., Terryn N., Hartley N., Bent E., Johnson S., Langham S.-A.,
RA McCullagh B., Robben J., Grymonprez B., Zimmermann W., Ramsperger U.,
RA Wedler H., Balke K., Wedler E., Peters S., van Staveren M., Dirkse W.,
RA Mooijman P., Klein Lankhorst R., Weitzenegger T., Bothe G., Rose M.,
RA Hauf J., Berneiser S., Hempel S., Feldpausch M., Lamberth S.,
RA Villarroel R., Gielen J., Ardiles W., Bents O., Lemcke K., Kolesov G.,
RA Mayer K.F.X., Rudd S., Schoof H., Schueller C., Zaccaria P., Mewes H.-W.,
RA Bevan M., Fransz P.F.;
RT "Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana.";
RL Nature 408:823-826(2000).
RN [4]
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 [5]
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 [6]
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 [7]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
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 (JUL-2006) to the EMBL/GenBank/DDBJ databases.
RN [8]
RP FUNCTION, AND SUBCELLULAR LOCATION.
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 [9]
RP FUNCTION, AND CATALYTIC ACTIVITY.
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 ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=22223895; DOI=10.1074/mcp.m111.015131;
RA Bienvenut W.V., Sumpton D., Martinez A., Lilla S., Espagne C., Meinnel T.,
RA Giglione C.;
RT "Comparative large-scale characterisation of plant vs. mammal proteins
RT reveals similar and idiosyncratic N-alpha acetylation features.";
RL Mol. Cell. Proteomics 11:M111.015131-M111.015131(2012).
CC -!- FUNCTION: Catalyzes the formation of pyridoxal 5'-phosphate from ribose
CC 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and ammonia. The
CC ammonia is provided by PDX2. Can also use ribulose 5-phosphate and
CC dihydroxyacetone phosphate as substrates, resulting from enzyme-
CC catalyzed isomerization of RBP and G3P, respectively. Also plays an
CC indirect role in resistance to singlet oxygen-generating
CC photosensitizers. {ECO:0000269|PubMed:16157873,
CC ECO:0000269|PubMed:16236150, 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 -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate biosynthesis.
CC -!- SUBUNIT: Homodimer or heterodimer with PDX1.1 or PDX1.2. Interacts with
CC PDX2. {ECO:0000269|PubMed:16766694}.
CC -!- INTERACTION:
CC Q8L940; Q9ZNR6: PDX12; NbExp=5; IntAct=EBI-1545956, EBI-1545987;
CC -!- SUBCELLULAR LOCATION: Cytoplasm. Cell membrane. Membrane.
CC -!- TISSUE SPECIFICITY: Expressed in cotyledons, rapidly dividing root
CC stele tissues, stems, leaves, flowers, mature pollen, and siliques.
CC {ECO:0000269|PubMed:16236150, ECO:0000269|PubMed:16766694}.
CC -!- INDUCTION: Not induced by cold, salt, drought or UV stress, or by
CC abscisic acid or jasmonic acid. {ECO:0000269|PubMed:16236150}.
CC -!- DISRUPTION PHENOTYPE: Plants have a lower leaf carotenoid and
CC chlorophyll a and b content, and are impaired both in root cell
CC division and in root cell elongation. Mutant rsr4-1 can be complemented
CC by the addition of any of the vitamin B6 vitamers, except pyridoxal 5'-
CC phosphate. {ECO:0000269|PubMed:16236150}.
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 PdxS/SNZ family. {ECO:0000305}.
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DR EMBL; AY972813; AAY42123.1; -; mRNA.
DR EMBL; AL161746; CAB81924.1; -; Genomic_DNA.
DR EMBL; CP002688; AED90340.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM69812.1; -; Genomic_DNA.
DR EMBL; AF428298; AAL16130.1; -; mRNA.
DR EMBL; AF446352; AAL48227.1; -; mRNA.
DR EMBL; AY097428; AAM19944.1; -; mRNA.
DR EMBL; AY088650; AAM66972.1; -; mRNA.
DR EMBL; AK227197; BAE99236.1; -; mRNA.
DR PIR; T48163; T48163.
DR RefSeq; NP_001331465.1; NM_001342589.1.
DR RefSeq; NP_195761.1; NM_120219.2.
DR PDB; 5K2Z; X-ray; 1.80 A; A/B/C/D=1-309.
DR PDB; 5K3V; X-ray; 1.90 A; A/B/C/D=1-309.
DR PDB; 5LNR; X-ray; 1.61 A; A/B/C/D=1-309.
DR PDB; 5LNS; X-ray; 1.91 A; A/B/C/D=1-309.
DR PDB; 5LNU; X-ray; 1.73 A; A/B/C/D=1-309.
DR PDB; 5LNV; X-ray; 2.24 A; A/B/C/D=1-309.
DR PDB; 5LNW; X-ray; 1.90 A; A/B/C/D=1-309.
DR PDB; 6HX3; X-ray; 2.00 A; B/D/F/H=21-290.
DR PDB; 6HXG; X-ray; 1.90 A; B/D/F/H=21-291.
DR PDB; 6HYE; X-ray; 2.53 A; B/D/F/H=1-309.
DR PDB; 7LB6; EM; 3.16 A; M/N/O/P/Q/R/S/T/U/V/W/X=2-309.
DR PDB; 7NHE; X-ray; 2.23 A; A/B/C/D=1-291.
DR PDB; 7NHF; X-ray; 2.35 A; A/B/C/D=1-291.
DR PDBsum; 5K2Z; -.
DR PDBsum; 5K3V; -.
DR PDBsum; 5LNR; -.
DR PDBsum; 5LNS; -.
DR PDBsum; 5LNU; -.
DR PDBsum; 5LNV; -.
DR PDBsum; 5LNW; -.
DR PDBsum; 6HX3; -.
DR PDBsum; 6HXG; -.
DR PDBsum; 6HYE; -.
DR PDBsum; 7LB6; -.
DR PDBsum; 7NHE; -.
DR PDBsum; 7NHF; -.
DR AlphaFoldDB; Q8L940; -.
DR SMR; Q8L940; -.
DR BioGRID; 17014; 9.
DR IntAct; Q8L940; 4.
DR STRING; 3702.AT5G01410.1; -.
DR iPTMnet; Q8L940; -.
DR MetOSite; Q8L940; -.
DR PaxDb; Q8L940; -.
DR PRIDE; Q8L940; -.
DR ProteomicsDB; 251389; -.
DR DNASU; 831738; -.
DR EnsemblPlants; AT5G01410.1; AT5G01410.1; AT5G01410.
DR EnsemblPlants; AT5G01410.2; AT5G01410.2; AT5G01410.
DR GeneID; 831738; -.
DR Gramene; AT5G01410.1; AT5G01410.1; AT5G01410.
DR Gramene; AT5G01410.2; AT5G01410.2; AT5G01410.
DR KEGG; ath:AT5G01410; -.
DR Araport; AT5G01410; -.
DR TAIR; locus:2179142; AT5G01410.
DR eggNOG; KOG1606; Eukaryota.
DR HOGENOM; CLU_055352_1_0_1; -.
DR InParanoid; Q8L940; -.
DR OMA; RYANRGW; -.
DR OrthoDB; 1090029at2759; -.
DR PhylomeDB; Q8L940; -.
DR UniPathway; UPA00245; -.
DR PRO; PR:Q8L940; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8L940; baseline and differential.
DR Genevisible; Q8L940; AT.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0012505; C:endomembrane system; IDA:TAIR.
DR GO; GO:0005886; C:plasma membrane; IDA:TAIR.
DR GO; GO:0016843; F:amine-lyase activity; IBA:GO_Central.
DR GO; GO:0046982; F:protein heterodimerization activity; IPI:TAIR.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:TAIR.
DR GO; GO:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
DR GO; GO:0006520; P:cellular amino acid metabolic process; IMP:TAIR.
DR GO; GO:0015994; P:chlorophyll metabolic process; IMP:TAIR.
DR GO; GO:0042538; P:hyperosmotic salinity response; IMP:TAIR.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
DR GO; GO:0006982; P:response to lipid hydroperoxide; IMP:TAIR.
DR GO; GO:0010335; P:response to non-ionic osmotic stress; IMP:TAIR.
DR GO; GO:0006979; P:response to oxidative stress; IMP:TAIR.
DR GO; GO:0009651; P:response to salt stress; IMP:TAIR.
DR GO; GO:0010224; P:response to UV-B; IGI:TAIR.
DR CDD; cd04727; pdxS; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_01824; PdxS; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR001852; PdxS/SNZ.
DR InterPro; IPR033755; PdxS/SNZ_N.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR PANTHER; PTHR31829; PTHR31829; 1.
DR Pfam; PF01680; SOR_SNZ; 1.
DR PIRSF; PIRSF029271; Pdx1; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
DR TIGRFAMs; TIGR00343; TIGR00343; 1.
DR PROSITE; PS01235; PDXS_SNZ_1; 1.
DR PROSITE; PS51129; PDXS_SNZ_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cell membrane; Cytoplasm; Lyase; Membrane;
KW Pyridoxal phosphate; Reference proteome; Schiff base.
FT CHAIN 1..309
FT /note="Pyridoxal 5'-phosphate synthase subunit PDX1.3"
FT /id="PRO_0000109368"
FT ACT_SITE 97
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 40
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 169
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 181
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250|UniProtKB:Q03148"
FT BINDING 230
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 251..252
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT MUTAGEN 54
FT /note="G->S: In rsr4-1; strongly reduced oligomerization
FT and 63% reduction in pyridoxal biosynthesis."
FT /evidence="ECO:0000269|PubMed:16766694"
FT CONFLICT 226
FT /note="F -> S (in Ref. 6; AAM66972)"
FT /evidence="ECO:0000305"
FT HELIX 22..30
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 31..33
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 36..43
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 44..52
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 65..70
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 80..89
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 94..99
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 103..112
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 115..120
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 141..147
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 148..157
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 160..164
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 168..170
FT /evidence="ECO:0007829|PDB:5LNU"
FT HELIX 174..192
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 195..197
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 198..205
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 209..218
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 222..227
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 234..243
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 246..250
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 253..256
FT /evidence="ECO:0007829|PDB:5LNR"
FT STRAND 257..259
FT /evidence="ECO:0007829|PDB:5LNS"
FT HELIX 260..272
FT /evidence="ECO:0007829|PDB:5LNR"
FT TURN 273..275
FT /evidence="ECO:0007829|PDB:5LNR"
FT HELIX 277..284
FT /evidence="ECO:0007829|PDB:5LNR"
SQ SEQUENCE 309 AA; 33216 MW; E74EBBCD4F124456 CRC64;
MEGTGVVAVY GNGAITEAKK SPFSVKVGLA QMLRGGVIMD VVNAEQARIA EEAGACAVMA
LERVPADIRA QGGVARMSDP QMIKEIKQAV TIPVMAKARI GHFVEAQILE AIGIDYIDES
EVLTLADEDH HINKHNFRIP FVCGCRNLGE ALRRIREGAA MIRTKGEAGT GNIIEAVRHV
RSVNGDIRVL RNMDDDEVFT FAKKLAAPYD LVMQTKQLGR LPVVQFAAGG VATPADAALM
MQLGCDGVFV GSGIFKSGDP ARRARAIVQA VTHYSDPEML VEVSCGLGEA MVGINLNDEK
VERFANRSE
