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 27-MAR-2024, entry version 158. 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}; CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- 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.Q9LTX3; -. DR iPTMnet; Q9LTX3; -. DR PaxDb; 3702-AT5G49970-1; -. 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; AT5G49970; PPOX. DR eggNOG; KOG2585; Eukaryota. DR eggNOG; KOG2586; Eukaryota. DR HOGENOM; CLU_032263_1_1_1; -. DR InParanoid; Q9LTX3; -. DR OMA; DPFDQFR; -. DR OrthoDB; 1493at2759; -. DR PhylomeDB; Q9LTX3; -. DR BioCyc; ARA:AT5G49970-MONOMER; -. DR BioCyc; MetaCyc:MONOMER-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 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; 3.40.50.10260; YjeF N-terminal domain; 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 NCBIfam; TIGR00558; pdxH; 1. DR NCBIfam; TIGR00197; yjeF_nterm; 1. DR PANTHER; PTHR10851:SF0; PYRIDOXINE-5'-PHOSPHATE OXIDASE; 1. DR PANTHER; PTHR10851; PYRIDOXINE-5-PHOSPHATE OXIDASE; 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; SSF50475; FMN-binding split barrel; 1. DR SUPFAM; SSF64153; YjeF N-terminal domain-like; 1. DR PROSITE; PS01064; PYRIDOX_OXIDASE; 1. DR PROSITE; PS51385; YJEF_N; 1. DR Genevisible; Q9LTX3; AT. 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 //