PPOX1_ARATH
ID PPOX1_ARATH Reviewed; 530 AA.
AC Q9LTX3; F4K7H2; Q8L7T7; Q8L9L3;
DT 09-JAN-2013, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2000, sequence version 1.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=Pyridoxine/pyridoxamine 5'-phosphate oxidase 1, chloroplastic;
DE Short=AtPPOX1;
DE Includes:
DE RecName: Full=Pyridoxine/pyridoxamine 5'-phosphate oxidase;
DE EC=1.4.3.5 {ECO:0000269|PubMed:17224143, ECO:0000269|PubMed:17873088};
DE AltName: Full=PNP/PMP oxidase;
DE Short=PNPOx;
DE AltName: Full=Pyridoxal 5'-phosphate synthase;
DE Includes:
DE RecName: Full=Probable NAD(P)HX epimerase;
DE EC=5.1.99.6 {ECO:0000305};
DE Flags: Precursor;
GN Name=PPOX1; Synonyms=PDX3, PDXH; OrderedLocusNames=At5g49970;
GN ORFNames=K9P8.11;
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=10718197; DOI=10.1093/dnares/7.1.31;
RA Sato S., Nakamura Y., Kaneko T., Katoh T., Asamizu E., Kotani H.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. X. Sequence
RT features of the regions of 3,076,755 bp covered by sixty P1 and TAC
RT clones.";
RL DNA Res. 7:31-63(2000).
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] OF 12-530 (ISOFORM 1).
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 NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 34-530 (ISOFORM 1).
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 [5]
RP FUNCTION AS PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, AND CATALYTIC
RP ACTIVITY.
RX PubMed=17224143; DOI=10.1016/j.febslet.2006.12.028;
RA Sang Y., Barbosa J.M., Wu H., Locy R.D., Singh N.K.;
RT "Identification of a pyridoxine (pyridoxamine) 5'-phosphate oxidase from
RT Arabidopsis thaliana.";
RL FEBS Lett. 581:344-348(2007).
RN [6]
RP FUNCTION AS PYRIDOXINE/PYRIDOXAMINE 5'-PHOSPHATE OXIDASE, AND CATALYTIC
RP ACTIVITY.
RX PubMed=17873088; DOI=10.1104/pp.107.105189;
RA Gonzalez E., Danehower D., Daub M.E.;
RT "Vitamer levels, stress response, enzyme activity, and gene regulation of
RT Arabidopsis lines mutant in the pyridoxine/pyridoxamine 5'-phosphate
RT oxidase (PDX3) and the pyridoxal kinase (SOS4) genes involved in the
RT vitamin B6 salvage pathway.";
RL Plant Physiol. 145:985-996(2007).
RN [7]
RP TISSUE SPECIFICITY, INDUCTION, ALTERNATIVE SPLICING, AND SUBCELLULAR
RP LOCATION.
RX PubMed=21051239; DOI=10.1016/j.plaphy.2010.10.003;
RA Sang Y., Locy R.D., Goertzen L.R., Rashotte A.M., Si Y., Kang K.,
RA Singh N.K.;
RT "Expression, in vivo localization and phylogenetic analysis of a pyridoxine
RT 5'-phosphate oxidase in Arabidopsis thaliana.";
RL Plant Physiol. Biochem. 49:88-95(2011).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-65, CLEAVAGE OF TRANSIT PEPTIDE
RP [LARGE SCALE ANALYSIS] AFTER ASN-64, 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 oxidation of either pyridoxine 5'-phosphate
CC (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate
CC (PLP). Involved in the PLP salvage pathway. Has a higher preference for
CC PNP over PMP. May also catalyze the epimerization of the S- and R-forms
CC of NAD(P)HX, a damaged form of NAD(P)H that is a result of enzymatic or
CC heat-dependent hydration. This is a prerequisite for the S-specific
CC NAD(P)H-hydrate dehydratase to allow the repair of both epimers of
CC NAD(P)HX. {ECO:0000269|PubMed:17224143, ECO:0000269|PubMed:17873088}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + O2 + pyridoxamine 5'-phosphate = H2O2 + NH4(+) +
CC pyridoxal 5'-phosphate; Xref=Rhea:RHEA:15817, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:15379, ChEBI:CHEBI:16240, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:58451, ChEBI:CHEBI:597326; EC=1.4.3.5;
CC Evidence={ECO:0000269|PubMed:17224143, ECO:0000269|PubMed:17873088};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=O2 + pyridoxine 5'-phosphate = H2O2 + pyridoxal 5'-phosphate;
CC Xref=Rhea:RHEA:15149, ChEBI:CHEBI:15379, ChEBI:CHEBI:16240,
CC ChEBI:CHEBI:58589, ChEBI:CHEBI:597326; EC=1.4.3.5;
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6R)-NADHX = (6S)-NADHX; Xref=Rhea:RHEA:32215,
CC ChEBI:CHEBI:64074, ChEBI:CHEBI:64075; EC=5.1.99.6;
CC Evidence={ECO:0000305};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6R)-NADPHX = (6S)-NADPHX; Xref=Rhea:RHEA:32227,
CC ChEBI:CHEBI:64076, ChEBI:CHEBI:64077; EC=5.1.99.6;
CC Evidence={ECO:0000305};
CC -!- COFACTOR:
CC Name=FMN; Xref=ChEBI:CHEBI:58210; Evidence={ECO:0000250};
CC Note=Binds 1 FMN per subunit. {ECO:0000250};
CC -!- COFACTOR:
CC Name=K(+); Xref=ChEBI:CHEBI:29103; Evidence={ECO:0000250};
CC Note=Binds 1 potassium ion per subunit. {ECO:0000250};
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxamine 5'-phosphate: step 1/1.
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxine 5'-phosphate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast
CC {ECO:0000269|PubMed:21051239}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q9LTX3-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q9LTX3-2; Sequence=VSP_044534, VSP_044535;
CC -!- TISSUE SPECIFICITY: Expressed in leaves, stems, flowers and roots.
CC {ECO:0000269|PubMed:21051239}.
CC -!- INDUCTION: Circadian regulation. Up-regulated by light, heat, jasmonic
CC acid, ethylene and abscisic acid treatments. Down-regulated by drought
CC and salt treatment. Not induced by UV irradiation.
CC {ECO:0000269|PubMed:21051239}.
CC -!- DOMAIN: Most plant PPOX proteins have both a pyridoxamine 5'-phosphate
CC oxidase domain and an extra YjeF N-terminal domain.
CC -!- MISCELLANEOUS: Mutants with reduced expression of PPOX1 (RNAi) have
CC lower levels of total B6 vitamers, a reduced growth and are sensitive
CC to high light. {ECO:0000305|PubMed:21051239}.
CC -!- MISCELLANEOUS: [Isoform 2]: Not detected in roots. {ECO:0000305}.
CC -!- SIMILARITY: In the N-terminal section; belongs to the NnrE/AIBP family.
CC {ECO:0000305}.
CC -!- SIMILARITY: In the C-terminal section; belongs to the pyridoxamine 5'-
CC phosphate oxidase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAM65907.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
CC Sequence=AAM83249.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
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DR EMBL; AB024032; BAA97018.1; -; Genomic_DNA.
DR EMBL; CP002688; AED95878.1; -; Genomic_DNA.
DR EMBL; CP002688; AED95879.1; -; Genomic_DNA.
DR EMBL; AY127025; AAM83249.1; ALT_INIT; mRNA.
DR EMBL; BT000605; AAN18174.1; -; mRNA.
DR EMBL; AY088368; AAM65907.1; ALT_INIT; mRNA.
DR RefSeq; NP_568717.2; NM_124376.4. [Q9LTX3-1]
DR RefSeq; NP_974918.1; NM_203189.2. [Q9LTX3-2]
DR AlphaFoldDB; Q9LTX3; -.
DR SMR; Q9LTX3; -.
DR BioGRID; 20307; 10.
DR STRING; 3702.AT5G49970.1; -.
DR iPTMnet; Q9LTX3; -.
DR PaxDb; Q9LTX3; -.
DR PRIDE; Q9LTX3; -.
DR ProteomicsDB; 236582; -. [Q9LTX3-1]
DR EnsemblPlants; AT5G49970.1; AT5G49970.1; AT5G49970. [Q9LTX3-1]
DR EnsemblPlants; AT5G49970.2; AT5G49970.2; AT5G49970. [Q9LTX3-2]
DR GeneID; 835061; -.
DR Gramene; AT5G49970.1; AT5G49970.1; AT5G49970. [Q9LTX3-1]
DR Gramene; AT5G49970.2; AT5G49970.2; AT5G49970. [Q9LTX3-2]
DR KEGG; ath:AT5G49970; -.
DR Araport; AT5G49970; -.
DR TAIR; locus:2158814; AT5G49970.
DR eggNOG; KOG2585; Eukaryota.
DR eggNOG; KOG2586; Eukaryota.
DR HOGENOM; CLU_032263_1_1_1; -.
DR OMA; PEFLEDQ; -.
DR OrthoDB; 982173at2759; -.
DR PhylomeDB; Q9LTX3; -.
DR BioCyc; ARA:AT5G49970-MON; -.
DR BioCyc; MetaCyc:MON-17901; -.
DR BRENDA; 5.1.99.6; 399.
DR UniPathway; UPA01068; UER00304.
DR UniPathway; UPA01068; UER00305.
DR PRO; PR:Q9LTX3; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9LTX3; baseline and differential.
DR Genevisible; Q9LTX3; AT.
DR GO; GO:0009507; C:chloroplast; IDA:TAIR.
DR GO; GO:0005829; C:cytosol; IDA:TAIR.
DR GO; GO:0005739; C:mitochondrion; IDA:TAIR.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0010181; F:FMN binding; IEA:InterPro.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0052856; F:NADHX epimerase activity; IDA:TAIR.
DR GO; GO:0052857; F:NADPHX epimerase activity; IDA:TAIR.
DR GO; GO:0004733; F:pyridoxamine-phosphate oxidase activity; IDA:TAIR.
DR GO; GO:0006734; P:NADH metabolic process; IMP:TAIR.
DR GO; GO:0006739; P:NADP metabolic process; IMP:TAIR.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; IEA:UniProtKB-KW.
DR Gene3D; 2.30.110.10; -; 1.
DR Gene3D; 3.40.50.10260; -; 1.
DR HAMAP; MF_01966; NADHX_epimerase; 1.
DR HAMAP; MF_01629; PdxH; 1.
DR InterPro; IPR000659; Pyridox_Oxase.
DR InterPro; IPR019740; Pyridox_Oxase_CS.
DR InterPro; IPR021198; Pyridox_Oxase_pln.
DR InterPro; IPR011576; Pyridox_Oxase_put.
DR InterPro; IPR019576; Pyridoxamine_oxidase_dimer_C.
DR InterPro; IPR012349; Split_barrel_FMN-bd.
DR InterPro; IPR004443; YjeF_N_dom.
DR InterPro; IPR036652; YjeF_N_dom_sf.
DR InterPro; IPR032976; YJEFN_prot_NAXE-like.
DR PANTHER; PTHR13232; PTHR13232; 1.
DR Pfam; PF10590; PNP_phzG_C; 1.
DR Pfam; PF01243; Putative_PNPOx; 1.
DR Pfam; PF03853; YjeF_N; 1.
DR PIRSF; PIRSF037048; PyrdxN_5-P_Oxase_ross-cont_pln; 1.
DR SUPFAM; SSF64153; SSF64153; 1.
DR TIGRFAMs; TIGR00558; pdxH; 1.
DR TIGRFAMs; TIGR00197; yjeF_nterm; 1.
DR PROSITE; PS01064; PYRIDOX_OXIDASE; 1.
DR PROSITE; PS51385; YJEF_N; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; Chloroplast; Flavoprotein; FMN;
KW Isomerase; Metal-binding; Multifunctional enzyme; NAD; Nucleotide-binding;
KW Oxidoreductase; Plastid; Potassium; Pyridoxine biosynthesis;
KW Reference proteome; Transit peptide.
FT TRANSIT 1..64
FT /note="Chloroplast"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 65..530
FT /note="Pyridoxine/pyridoxamine 5'-phosphate oxidase 1,
FT chloroplastic"
FT /id="PRO_0000420549"
FT DOMAIN 81..297
FT /note="YjeF N-terminal"
FT BINDING 131..135
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000250"
FT BINDING 132
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250"
FT BINDING 196
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250"
FT BINDING 200..206
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000250"
FT BINDING 238
FT /ligand="(6S)-NADPHX"
FT /ligand_id="ChEBI:CHEBI:64076"
FT /evidence="ECO:0000250"
FT BINDING 241
FT /ligand="K(+)"
FT /ligand_id="ChEBI:CHEBI:29103"
FT /evidence="ECO:0000250"
FT BINDING 247..250
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 321..324
FT /ligand="substrate"
FT /evidence="ECO:0000250"
FT BINDING 325..327
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 374..377
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 379
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 389..390
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 395..396
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 418
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 436
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 440
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 444
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 453..454
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:Q9NVS9"
FT BINDING 499
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 505..507
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT BINDING 509
FT /ligand="FMN"
FT /ligand_id="ChEBI:CHEBI:58210"
FT /evidence="ECO:0000250|UniProtKB:P0AFI7"
FT MOD_RES 65
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:22223895"
FT VAR_SEQ 261..271
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_044534"
FT VAR_SEQ 478..530
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_044535"
FT CONFLICT 241
FT /note="S -> Y (in Ref. 4; AAM65907)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 530 AA; 59376 MW; 22E8DFEC1A2167EE CRC64;
MRNVIRRVTT MTFTFLLQSP PLPISPSPPQ FSLSSSPLSK TQRFITPSQG SRLRTLCTKV
IIPNMQDSGS PPLSYLTQRE AAEIDETLMG PLGFSIDQLM ELAGLSVAAS IAEVYKPEEY
SRVLAICGPG NNGGDGLVAA RHLHHFGYKP FICYPKRTAK PLYTGLVTQL DSLSVPFVSV
EDLPDDLSKD FDVIVDAMFG FSFHGAPRPP FDDLIRRLVS LQNYEQTLQK HPVIVSVDIP
SGWHVEEGDH EDGGIKPDML VSLTAPKLCA KRFRGPHHFL GGRFVPPSVA EKYKLELPSY
PGTSMCVRIG KPPKVDISAM RVNYVSPELL EEQVETDPTV QFRKWFDEAV AAGLRETNAM
ALSTANKDKK PSSRMVLLKG FDENGFVWFT NYESKKGSDL SENPSAALLF YWEILNRQVR
IEGPVERIPE SESENYFHSR PRGSQIGAIV SKQSSVVPGR HVLYDEYEEL TKQYSDGSVI
PKPKNWGGFR LKPNLFEFWQ GQPSRLHDRL QYSLQDVNGN PAWKIHRLAP
