(data stored in ACNUC13479 zone)

SWISSPROT: 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   08-MAY-2019, entry version 130.
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; Magnoliophyta; eudicotyledons; Gunneridae;
OC   Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae;
OC   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
RT   tolerance 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.,
RA   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
RT   vitamin 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.,
RA   Kohara M., Matsumoto M., Matsuno A., Muraki A., Nakayama S.,
RA   Nakazaki N., Naruo K., Okumura S., Shinpo S., Takeuchi C., Wada T.,
RA   Watanabe A., Yamada M., Yasuda M., Sato S., de la Bastide M.,
RA   Huang E., Spiegel L., Gnoj L., O'Shaughnessy A., Preston R.,
RA   Habermann K., Murray J., Johnson D., Rohlfing T., Nelson J.,
RA   Stoneking T., Pepin K., Spieth J., Sekhon M., Armstrong J., Becker M.,
RA   Belter E., Cordum H., Cordes M., Courtney L., Courtney W., Dante M.,
RA   Du H., Edwards J., Fryman J., Haakensen B., Lamar E., Latreille P.,
RA   Leonard S., Meyer R., Mulvaney E., Ozersky P., Riley A., Strowmatt C.,
RA   Wagner-McPherson C., Wollam A., Yoakum M., Bell M., Dedhia N.,
RA   Parnell L., Shah R., Rodriguez M., Hoon See L., Vil D., Baker J.,
RA   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.,
RA   Langham S.-A., McCullagh B., Robben J., Grymonprez B., Zimmermann W.,
RA   Ramsperger U., Wedler H., Balke K., Wedler E., Peters S.,
RA   van Staveren M., Dirkse W., Mooijman P., Klein Lankhorst R.,
RA   Weitzenegger T., Bothe G., Rose M., Hauf J., Berneiser S., Hempel S.,
RA   Feldpausch M., Lamberth S., Villarroel R., Gielen J., Ardiles W.,
RA   Bents O., Lemcke K., Kolesov G., Mayer K.F.X., Rudd S., Schoof H.,
RA   Schueller C., Zaccaria P., Mewes H.-W., Bevan M., Fransz P.F.;
RT   "Sequence and analysis of chromosome 5 of the plant Arabidopsis
RT   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
RT   reference 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.,
RA   Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F.,
RA   Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.,
RA   Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J.,
RA   Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y.,
RA   Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P.,
RA   Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F.,
RA   Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M.,
RA   Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J.,
RA   Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T.,
RA   Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y.,
RA   Yuan S., Shinozaki K., Davis R.W., Theologis A., 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.,
RA   Hayashizaki Y., 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
RT   in vitamin B6 biosynthesis.";
RL   Plant Physiol. 144:915-925(2007).
RN   [10]
RP   ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY
RP   MASS 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.,
RA   Meinnel T., 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
CC       ribose 5-phosphate (RBP), glyceraldehyde 3-phosphate (G3P) and
CC       ammonia. The ammonia is provided by PDX2. Can also use ribulose 5-
CC       phosphate and dihydroxyacetone phosphate as substrates, resulting
CC       from enzyme-catalyzed isomerization of RBP and G3P, respectively.
CC       Also plays an indirect role in resistance to singlet oxygen-
CC       generating 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-
CC         phosphate + L-glutamine = H(+) + 3 H2O + L-glutamate + phosphate
CC         + pyridoxal 5'-phosphate; Xref=Rhea:RHEA:31507,
CC         ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29985,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:58273, ChEBI:CHEBI:58359,
CC         ChEBI:CHEBI:59776, ChEBI:CHEBI:597326; EC=4.3.3.6;
CC         Evidence={ECO:0000269|PubMed:17468224};
CC   -!- PATHWAY: Cofactor biosynthesis; pyridoxal 5'-phosphate
CC       biosynthesis.
CC   -!- SUBUNIT: Homodimer or heterodimer with PDX1.1 or PDX1.2. Interacts
CC       with PDX2. {ECO:0000269|PubMed:16766694}.
CC   -!- INTERACTION:
CC       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
CC       siliques. {ECO:0000269|PubMed:16236150,
CC       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
CC       complemented by the addition of any of the vitamin B6 vitamers,
CC       except pyridoxal 5'-phosphate. {ECO:0000269|PubMed:16236150}.
CC   -!- MISCELLANEOUS: Vitamin B6 is an essential quencher of singlet
CC       oxygen in plants, that can protect cellular membranes from lipid
CC       peroxidation.
CC   -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000305}.
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   PDBsum; 5K2Z; -.
DR   PDBsum; 5K3V; -.
DR   PDBsum; 5LNR; -.
DR   PDBsum; 5LNS; -.
DR   PDBsum; 5LNU; -.
DR   PDBsum; 5LNV; -.
DR   PDBsum; 5LNW; -.
DR   SMR; Q8L940; -.
DR   BioGrid; 17014; 6.
DR   IntAct; Q8L940; 4.
DR   STRING; 3702.AT5G01410.1; -.
DR   iPTMnet; Q8L940; -.
DR   PaxDb; Q8L940; -.
DR   PRIDE; Q8L940; -.
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   eggNOG; COG0214; LUCA.
DR   HOGENOM; HOG000227586; -.
DR   InParanoid; Q8L940; -.
DR   KO; K06215; -.
DR   OMA; IGVDMID; -.
DR   OrthoDB; 1090029at2759; -.
DR   PhylomeDB; Q8L940; -.
DR   BioCyc; ARA:GQT-915-MONOMER; -.
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;
DR   PRODOM; Q8L940.
DR   SWISS-2DPAGE; Q8L940.
KW   3D-structure; Acetylation; Cell membrane; Complete proteome;
KW   Cytoplasm; Lyase; Membrane; Pyridoxal phosphate; Reference proteome;
KW   Schiff base.
FT   CHAIN         1    309       Pyridoxal 5'-phosphate synthase subunit
FT                                PDX1.3.
FT                                /FTId=PRO_0000109368.
FT   REGION      251    252       D-ribose 5-phosphate binding.
FT                                {ECO:0000250|UniProtKB:O59080}.
FT   ACT_SITE     97     97       Schiff-base intermediate with D-ribose 5-
FT                                phosphate.
FT                                {ECO:0000250|UniProtKB:O59080}.
FT   BINDING      40     40       D-ribose 5-phosphate.
FT                                {ECO:0000250|UniProtKB:O59080}.
FT   BINDING     169    169       D-ribose 5-phosphate; via amide nitrogen.
FT                                {ECO:0000250|UniProtKB:O59080}.
FT   BINDING     181    181       Glyceraldehyde 3-phosphate.
FT                                {ECO:0000250|UniProtKB:Q03148}.
FT   BINDING     230    230       D-ribose 5-phosphate; via amide nitrogen.
FT                                {ECO:0000250|UniProtKB:O59080}.
FT   MOD_RES       1      1       N-acetylmethionine.
FT                                {ECO:0000244|PubMed:22223895}.
FT   MUTAGEN      54     54       G->S: In rsr4-1; strongly reduced
FT                                oligomerization and 63% reduction in
FT                                pyridoxal biosynthesis.
FT                                {ECO:0000269|PubMed:16766694}.
FT   CONFLICT    226    226       F -> S (in Ref. 6; AAM66972).
FT                                {ECO:0000305}.
FT   HELIX        22     30       {ECO:0000244|PDB:5LNR}.
FT   HELIX        31     33       {ECO:0000244|PDB:5LNR}.
FT   STRAND       36     43       {ECO:0000244|PDB:5LNR}.
FT   HELIX        44     52       {ECO:0000244|PDB:5LNR}.
FT   STRAND       56     60       {ECO:0000244|PDB:5LNR}.
FT   HELIX        65     70       {ECO:0000244|PDB:5LNR}.
FT   HELIX        80     89       {ECO:0000244|PDB:5LNR}.
FT   STRAND       94     99       {ECO:0000244|PDB:5LNR}.
FT   HELIX       103    112       {ECO:0000244|PDB:5LNR}.
FT   STRAND      115    120       {ECO:0000244|PDB:5LNR}.
FT   HELIX       134    136       {ECO:0000244|PDB:5LNR}.
FT   STRAND      141    147       {ECO:0000244|PDB:5LNR}.
FT   HELIX       148    157       {ECO:0000244|PDB:5LNR}.
FT   STRAND      160    164       {ECO:0000244|PDB:5LNR}.
FT   STRAND      168    170       {ECO:0000244|PDB:5LNU}.
FT   HELIX       174    192       {ECO:0000244|PDB:5LNR}.
FT   HELIX       195    197       {ECO:0000244|PDB:5LNR}.
FT   HELIX       198    205       {ECO:0000244|PDB:5LNR}.
FT   HELIX       209    218       {ECO:0000244|PDB:5LNR}.
FT   STRAND      222    227       {ECO:0000244|PDB:5LNR}.
FT   HELIX       234    243       {ECO:0000244|PDB:5LNR}.
FT   STRAND      246    250       {ECO:0000244|PDB:5LNR}.
FT   HELIX       253    256       {ECO:0000244|PDB:5LNR}.
FT   STRAND      257    259       {ECO:0000244|PDB:5LNS}.
FT   HELIX       260    272       {ECO:0000244|PDB:5LNR}.
FT   TURN        273    275       {ECO:0000244|PDB:5LNR}.
FT   HELIX       277    284       {ECO:0000244|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
//

If you have problems or comments...

PBIL Back to PBIL home page