PDX11_ARATH
ID PDX11_ARATH Reviewed; 309 AA.
AC O80448;
DT 15-MAR-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1998, sequence version 1.
DT 03-AUG-2022, entry version 151.
DE RecName: Full=Pyridoxal 5'-phosphate synthase subunit PDX1.1;
DE Short=AtPDX1.1;
DE Short=AtPDX1;2;
DE Short=PLP synthase subunit PDX1.1;
DE EC=4.3.3.6 {ECO:0000269|PubMed:17468224};
DE AltName: Full=HEVER-like protein;
GN Name=PDX11; Synonyms=PDX1L1; OrderedLocusNames=At2g38230;
GN ORFNames=F16M14.16;
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=10617197; DOI=10.1038/45471;
RA Lin X., Kaul S., Rounsley S.D., Shea T.P., Benito M.-I., Town C.D.,
RA Fujii C.Y., Mason T.M., Bowman C.L., Barnstead M.E., Feldblyum T.V.,
RA Buell C.R., Ketchum K.A., Lee J.J., Ronning C.M., Koo H.L., Moffat K.S.,
RA Cronin L.A., Shen M., Pai G., Van Aken S., Umayam L., Tallon L.J.,
RA Gill J.E., Adams M.D., Carrera A.J., Creasy T.H., Goodman H.M.,
RA Somerville C.R., Copenhaver G.P., Preuss D., Nierman W.C., White O.,
RA Eisen J.A., Salzberg S.L., Fraser C.M., Venter J.C.;
RT "Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana.";
RL Nature 402:761-768(1999).
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=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 [4]
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 [5]
RP TISSUE SPECIFICITY, AND INTERACTION WITH PDX1.2; PDX1.3 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 [6]
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).
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: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 PDX1.2 or PDX1.3. Interacts with
CC PDX2. {ECO:0000269|PubMed:16766694}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:16157873}.
CC -!- TISSUE SPECIFICITY: Expressed in flowers, shoots, leaves and weakly in
CC roots. {ECO:0000269|PubMed:16766694}.
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; AC003028; AAC27172.1; -; Genomic_DNA.
DR EMBL; CP002685; AEC09511.1; -; Genomic_DNA.
DR EMBL; AF370296; AAK44111.1; -; mRNA.
DR EMBL; AF385694; AAK60287.1; -; mRNA.
DR EMBL; AY063043; AAL34217.1; -; mRNA.
DR PIR; T01255; T01255.
DR RefSeq; NP_181358.1; NM_129380.3.
DR PDB; 5LNT; X-ray; 2.32 A; A/B/C/D=1-309.
DR PDBsum; 5LNT; -.
DR AlphaFoldDB; O80448; -.
DR SMR; O80448; -.
DR BioGRID; 3744; 7.
DR IntAct; O80448; 3.
DR STRING; 3702.AT2G38230.1; -.
DR iPTMnet; O80448; -.
DR PaxDb; O80448; -.
DR PRIDE; O80448; -.
DR ProteomicsDB; 251375; -.
DR DNASU; 818402; -.
DR EnsemblPlants; AT2G38230.1; AT2G38230.1; AT2G38230.
DR GeneID; 818402; -.
DR Gramene; AT2G38230.1; AT2G38230.1; AT2G38230.
DR KEGG; ath:AT2G38230; -.
DR Araport; AT2G38230; -.
DR TAIR; locus:2042932; AT2G38230.
DR eggNOG; KOG1606; Eukaryota.
DR HOGENOM; CLU_055352_1_0_1; -.
DR InParanoid; O80448; -.
DR OMA; HYNDAHV; -.
DR OrthoDB; 1090029at2759; -.
DR PhylomeDB; O80448; -.
DR BioCyc; ARA:AT2G38230-MON; -.
DR BioCyc; MetaCyc:AT2G38230-MON; -.
DR UniPathway; UPA00245; -.
DR PRO; PR:O80448; -.
DR Proteomes; UP000006548; Chromosome 2.
DR ExpressionAtlas; O80448; baseline and differential.
DR Genevisible; O80448; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005783; C:endoplasmic reticulum; HDA: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:0036381; F:pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity; IEA:UniProtKB-EC.
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 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; Cytoplasm; Lyase; Pyridoxal phosphate;
KW Reference proteome; Schiff base.
FT CHAIN 1..309
FT /note="Pyridoxal 5'-phosphate synthase subunit PDX1.1"
FT /id="PRO_0000109366"
FT ACT_SITE 98
FT /note="Schiff-base intermediate with D-ribose 5-phosphate"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 41
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 170
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 182
FT /ligand="D-glyceraldehyde 3-phosphate"
FT /ligand_id="ChEBI:CHEBI:59776"
FT /evidence="ECO:0000250|UniProtKB:Q03148"
FT BINDING 231
FT /ligand="D-ribose 5-phosphate"
FT /ligand_id="ChEBI:CHEBI:78346"
FT /evidence="ECO:0000250|UniProtKB:O59080"
FT BINDING 252..253
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:0000250|UniProtKB:Q8L940"
FT HELIX 23..31
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 32..34
FT /evidence="ECO:0007829|PDB:5LNT"
FT STRAND 38..44
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 45..53
FT /evidence="ECO:0007829|PDB:5LNT"
FT STRAND 57..61
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 66..72
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 81..90
FT /evidence="ECO:0007829|PDB:5LNT"
FT STRAND 95..100
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 104..112
FT /evidence="ECO:0007829|PDB:5LNT"
FT STRAND 116..121
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 135..137
FT /evidence="ECO:0007829|PDB:5LNT"
FT STRAND 142..148
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 149..158
FT /evidence="ECO:0007829|PDB:5LNT"
FT STRAND 161..166
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 175..192
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 196..198
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 199..205
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 210..219
FT /evidence="ECO:0007829|PDB:5LNT"
FT STRAND 223..230
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 235..243
FT /evidence="ECO:0007829|PDB:5LNT"
FT STRAND 247..253
FT /evidence="ECO:0007829|PDB:5LNT"
FT TURN 254..257
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 261..273
FT /evidence="ECO:0007829|PDB:5LNT"
FT TURN 274..276
FT /evidence="ECO:0007829|PDB:5LNT"
FT HELIX 278..285
FT /evidence="ECO:0007829|PDB:5LNT"
SQ SEQUENCE 309 AA; 32862 MW; 10D9EEDAEDC0BC4C CRC64;
MAGTGVVAVY GEGAMTETKQ KSPFSVKVGL AQMLRGGVIM DVVNAEQARI AEEAGACAVM
ALERVPADIR AQGGVARMSD PEMIKEIKNA VTIPVMAKAR IGHFVEAQIL EAIGVDYVDE
SEVLTLADED NHINKHNFKI PFVCGCRNLG EALRRIREGA AMIRTKGEAG TGNVVEAVRH
VRSVNGAIRL LRSMDDDEVF TYAKKIAAPY DLVVQTKELG RLPVVQFAAG GVATPADAAL
MMQLGCDGVF VGSGVFKSGD PVKRAKAIVQ AVTNYRDAAV LAEVSCGLGE AMVGLNLDDK
VERFASRSE
