PDX12_ARATH
ID PDX12_ARATH Reviewed; 314 AA.
AC Q9ZNR6; Q0WS48;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-1999, sequence version 1.
DT 25-MAY-2022, entry version 147.
DE RecName: Full=Pyridoxal 5'-phosphate synthase-like subunit PDX1.2;
DE Short=AtPDX1.2;
DE Short=AtPDX1;3;
GN Name=PDX12; Synonyms=A37, PDX1L2; OrderedLocusNames=At3g16050;
GN ORFNames=MSL1.3;
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 [MRNA], AND TISSUE SPECIFICITY.
RC STRAIN=cv. Columbia;
RA Oekresz L., Mathe C., Horvath E., Schell J., Koncz C., Szabados L.;
RT "T-DNA trapping of a cryptic promoter identifies an ortholog of highly
RT conserved SNZ growth arrest response genes in Arabidopsis.";
RL Plant Sci. 138:217-228(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=10819329; DOI=10.1093/dnares/7.2.131;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 3. I. Sequence
RT features of the regions of 4,504,864 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:131-135(2000).
RN [3]
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 [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].
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 [6]
RP 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 [7]
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 [8]
RP FUNCTION.
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 [9]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT ALA-2, CLEAVAGE OF INITIATOR
RP METHIONINE [LARGE SCALE ANALYSIS], AND IDENTIFICATION BY MASS SPECTROMETRY
RP [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: The protein has no function in the formation of pyridoxal 5'-
CC phosphate. {ECO:0000269|PubMed:17468224}.
CC -!- SUBUNIT: Homodimer or heterodimer with PDX1.1 or PDX1.3. No interaction
CC with PDX2.
CC -!- INTERACTION:
CC Q9ZNR6; Q8L940: PDX13; NbExp=5; IntAct=EBI-1545987, EBI-1545956;
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16157873}.
CC -!- TISSUE SPECIFICITY: Expressed in callus tissues, flowers and roots.
CC Weakly expressed in leaves and stems. {ECO:0000269|PubMed:16766694,
CC ECO:0000269|Ref.1}.
CC -!- MISCELLANEOUS: Unlike PDX1.1 or PDX1.3, PDX1.2 is unable to interact
CC with PDX2 and restore prototrophy in yeast snz1 mutants.
CC -!- SIMILARITY: Belongs to the PdxS/SNZ family. {ECO:0000305}.
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DR EMBL; AF029980; AAD01897.1; -; mRNA.
DR EMBL; AF029981; AAD01898.1; -; Genomic_DNA.
DR EMBL; AB012247; BAB02670.1; -; Genomic_DNA.
DR EMBL; CP002686; AEE75766.1; -; Genomic_DNA.
DR EMBL; BT003136; AAO24568.1; -; mRNA.
DR EMBL; AK228092; BAF00051.1; -; mRNA.
DR RefSeq; NP_188226.1; NM_112475.3.
DR PDB; 6HX3; X-ray; 2.00 A; A/C/E/G=1-314.
DR PDB; 6HXG; X-ray; 1.90 A; A/C/E/G=1-314.
DR PDB; 6HYE; X-ray; 2.53 A; A/C/E/G=1-314.
DR PDB; 7LB5; EM; 3.16 A; A/B/C/D/E/F/G/H/I/J/K/L=2-314.
DR PDB; 7LB6; EM; 3.16 A; A/B/C/D/E/F/G/H/I/J/K/L=2-314.
DR PDBsum; 6HX3; -.
DR PDBsum; 6HXG; -.
DR PDBsum; 6HYE; -.
DR PDBsum; 7LB5; -.
DR PDBsum; 7LB6; -.
DR AlphaFoldDB; Q9ZNR6; -.
DR SMR; Q9ZNR6; -.
DR BioGRID; 6184; 5.
DR IntAct; Q9ZNR6; 2.
DR STRING; 3702.AT3G16050.1; -.
DR iPTMnet; Q9ZNR6; -.
DR MetOSite; Q9ZNR6; -.
DR PaxDb; Q9ZNR6; -.
DR PRIDE; Q9ZNR6; -.
DR ProteomicsDB; 251004; -.
DR DNASU; 820850; -.
DR EnsemblPlants; AT3G16050.1; AT3G16050.1; AT3G16050.
DR GeneID; 820850; -.
DR Gramene; AT3G16050.1; AT3G16050.1; AT3G16050.
DR KEGG; ath:AT3G16050; -.
DR Araport; AT3G16050; -.
DR TAIR; locus:2093427; AT3G16050.
DR eggNOG; KOG1606; Eukaryota.
DR HOGENOM; CLU_055352_1_0_1; -.
DR OMA; CSDPYKR; -.
DR OrthoDB; 1090029at2759; -.
DR PhylomeDB; Q9ZNR6; -.
DR PRO; PR:Q9ZNR6; -.
DR Proteomes; UP000006548; Chromosome 3.
DR ExpressionAtlas; Q9ZNR6; baseline and differential.
DR Genevisible; Q9ZNR6; AT.
DR GO; GO:0005829; C:cytosol; 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:0006520; P:cellular amino acid metabolic process; IBA:GO_Central.
DR GO; GO:0042823; P:pyridoxal phosphate biosynthetic process; IBA:GO_Central.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IBA:GO_Central.
DR Gene3D; 3.20.20.70; -; 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 PROSITE; PS01235; PDXS_SNZ_1; 1.
DR PROSITE; PS51129; PDXS_SNZ_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Cytoplasm; Pyridoxal phosphate;
KW Reference proteome.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..314
FT /note="Pyridoxal 5'-phosphate synthase-like subunit PDX1.2"
FT /id="PRO_0000109367"
FT MOD_RES 2
FT /note="N-acetylalanine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT HELIX 31..38
FT /evidence="ECO:0007829|PDB:7LB5"
FT STRAND 44..49
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 52..61
FT /evidence="ECO:0007829|PDB:7LB5"
FT STRAND 64..68
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 84..93
FT /evidence="ECO:0007829|PDB:7LB5"
FT STRAND 98..103
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 107..115
FT /evidence="ECO:0007829|PDB:7LB5"
FT STRAND 119..127
FT /evidence="ECO:0007829|PDB:7LB5"
FT STRAND 145..151
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 152..161
FT /evidence="ECO:0007829|PDB:7LB5"
FT STRAND 164..169
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 179..197
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 200..202
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 203..210
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 214..223
FT /evidence="ECO:0007829|PDB:7LB5"
FT STRAND 227..235
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 239..247
FT /evidence="ECO:0007829|PDB:7LB5"
FT STRAND 251..255
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 257..259
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 265..277
FT /evidence="ECO:0007829|PDB:7LB5"
FT TURN 278..280
FT /evidence="ECO:0007829|PDB:7LB5"
FT HELIX 282..288
FT /evidence="ECO:0007829|PDB:7LB5"
SQ SEQUENCE 314 AA; 33836 MW; D894BC393CBBBA6A CRC64;
MADQAMTDQD QGAVTLYSGT AITDAKKNHP FSVKVGLAQV LRGGAIVEVS SVNQAKLAES
AGACSVIVSD PVRSRGGVRR MPDPVLIKEV KRAVSVPVMA RARVGHFVEA QILESLAVDY
IDESEIISVA DDDHFINKHN FRSPFICGCR DTGEALRRIR EGAAMIRIQG DLTATGNIAE
TVKNVRSLMG EVRVLNNMDD DEVFTFAKKI SAPYDLVAQT KQMGRVPVVQ FASGGITTPA
DAALMMQLGC DGVFVGSEVF DGPDPFKKLR SIVQAVQHYN DPHVLAEMSS GLENAMESLN
VRGDRIQDFG QGSV
