PDXK_ARATH
ID PDXK_ARATH Reviewed; 309 AA.
AC Q8W1X2; Q94EN4; Q9FKE1;
DT 06-DEC-2002, integrated into UniProtKB/Swiss-Prot.
DT 06-DEC-2002, sequence version 2.
DT 03-AUG-2022, entry version 143.
DE RecName: Full=Pyridoxal kinase {ECO:0000303|PubMed:12244454};
DE EC=2.7.1.35 {ECO:0000269|PubMed:12244454};
DE AltName: Full=Protein SALT OVERLY SENSITIVE 4 {ECO:0000303|PubMed:11910005, ECO:0000303|PubMed:12068103};
DE AltName: Full=Pyridoxal kinase-like protein SOS4 {ECO:0000303|PubMed:11910005};
DE AltName: Full=Pyridoxine kinase {ECO:0000303|PubMed:12244454};
DE Contains:
DE RecName: Full=Pyridoxal kinase, N-terminally processed {ECO:0000303|PubMed:12244454};
GN Name=PK {ECO:0000303|PubMed:12244454};
GN Synonyms=PDXK, SOS4 {ECO:0000303|PubMed:11910005,
GN ECO:0000303|PubMed:12068103};
GN OrderedLocusNames=At5g37850 {ECO:0000312|Araport:AT5G37850};
GN ORFNames=K18L3.2 {ECO:0000312|EMBL:BAB09031.1};
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] (ISOFORM 1), PROTEIN SEQUENCE OF 1-12, FUNCTION,
RP BIOPHYSICOCHEMICAL PROPERTIES, CATALYTIC ACTIVITY, PATHWAY, TISSUE
RP SPECIFICITY, DEVELOPMENTAL STAGE, AND HOMODIMERIZATION.
RC STRAIN=cv. Columbia;
RX PubMed=12244454; DOI=10.1007/s00425-002-0799-0;
RA Lum H.-K., Kwok F., Lo S.C.L.;
RT "Cloning and characterization of Arabidopsis thaliana pyridoxal kinase.";
RL Planta 215:870-879(2002).
RN [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS 1 AND 2), DISRUPTION PHENOTYPE,
RP TISSUE SPECIFICITY, FUNCTION, AND INDUCTION.
RC STRAIN=cv. Columbia;
RX PubMed=11910005; DOI=10.1105/tpc.010417;
RA Shi H., Xiong L., Stevenson B., Lu T., Zhu J.-K.;
RT "The Arabidopsis salt overly sensitive 4 mutants uncover a critical role
RT for vitamin B6 in plant salt tolerance.";
RL Plant Cell 14:575-588(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9734815; DOI=10.1093/dnares/5.3.203;
RA Kotani H., Nakamura Y., Sato S., Asamizu E., Kaneko T., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence
RT features of the regions of 1,367,185 bp covered by 19 physically assigned
RT P1 and TAC clones.";
RL DNA Res. 5:203-216(1998).
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 reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (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 [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (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 [7]
RP FUNCTION, DISRUPTION PHENOTYPE, AND TISSUE SPECIFICITY.
RX PubMed=12068103; DOI=10.1104/pp.001982;
RA Shi H., Zhu J.-K.;
RT "SOS4, a pyridoxal kinase gene, is required for root hair development in
RT Arabidopsis.";
RL Plant Physiol. 129:585-593(2002).
RN [8]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT THR-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: Catalyzes the transfer of a phosphate group from ATP to the
CC 5-hydroxylmethyl group of pyridoxal to form the biologically active
CC pyridoxal phosphate, an active form of vitamin B6 (PubMed:12068103,
CC PubMed:12244454). Required for Na(+) and K(+) homeostasis and for salt
CC tolerance (PubMed:11910005). Involved in root hair development, both
CC for initiation and tip growth (PubMed:12068103).
CC {ECO:0000269|PubMed:11910005, ECO:0000269|PubMed:12068103,
CC ECO:0000269|PubMed:12244454}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + pyridoxal = ADP + H(+) + pyridoxal 5'-phosphate;
CC Xref=Rhea:RHEA:10224, ChEBI:CHEBI:15378, ChEBI:CHEBI:17310,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:456216, ChEBI:CHEBI:597326;
CC EC=2.7.1.35; Evidence={ECO:0000269|PubMed:12244454};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12244454};
CC Note=Divalent metal cations. Zn(2+) >> Co(2+) > Mg(2+) > Mn(2+) >
CC Ca(2+). {ECO:0000269|PubMed:12244454};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=98 uM for ATP {ECO:0000269|PubMed:12244454};
CC KM=688 uM for pyridoxal {ECO:0000269|PubMed:12244454};
CC Vmax=1.604 mmol/min/mg enzyme {ECO:0000269|PubMed:12244454};
CC pH dependence:
CC Optimum pH is 6.0. Active from pH 4.5 to 10.5.
CC {ECO:0000269|PubMed:12244454};
CC -!- PATHWAY: Cofactor metabolism; pyridoxal 5'-phosphate salvage; pyridoxal
CC 5'-phosphate from pyridoxal: step 1/1. {ECO:0000269|PubMed:12244454}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:12244454}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8W1X2-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8W1X2-2; Sequence=VSP_004654;
CC -!- TISSUE SPECIFICITY: Expressed ubiquitously in leaves, stems, roots,
CC flowers and siliques (PubMed:12244454). Present in root hairs and other
CC tip-growing cells such as papillar cells on the top of stigma
CC (PubMed:12068103). {ECO:0000269|PubMed:12068103,
CC ECO:0000269|PubMed:12244454}.
CC -!- DEVELOPMENTAL STAGE: Becomes detectable 60 hours after imbibition of
CC the seeds and remains constant up to 101 hours after imbibition.
CC {ECO:0000269|PubMed:12244454}.
CC -!- INDUCTION: Both long and short transcripts are down-regulated in roots
CC but not in shoots by NaCl and abscisic acid treatment
CC (PubMed:11910005). Under cold stress, the expression of the short
CC transcript is increased while the long one becomes undetectable
CC (PubMed:11910005). {ECO:0000269|PubMed:11910005}.
CC -!- DISRUPTION PHENOTYPE: Defective pyridoxal kinase results in both salt
CC hypersensitive and root hairless phenotypes (PubMed:11910005,
CC PubMed:12068103). Hypersensitivity to Na(+), K(+) and Li(+) ions
CC (PubMed:11910005). Increased accumulation of Na(+) ions but reduced
CC K(+) retaining under NaCl stress (PubMed:11910005).
CC {ECO:0000269|PubMed:11910005, ECO:0000269|PubMed:12068103}.
CC -!- SIMILARITY: Belongs to the pyridoxine kinase family. {ECO:0000305}.
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DR EMBL; AF404865; AAL57364.2; -; mRNA.
DR EMBL; AF400125; AAK94020.1; -; Genomic_DNA.
DR EMBL; AF400125; AAK94021.1; -; Genomic_DNA.
DR EMBL; AB012241; BAB09031.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94239.1; -; Genomic_DNA.
DR EMBL; CP002688; AED94240.1; -; Genomic_DNA.
DR EMBL; CP002688; ANM69628.1; -; Genomic_DNA.
DR EMBL; AY136333; AAM96999.1; -; mRNA.
DR EMBL; BT008815; AAP68254.1; -; mRNA.
DR EMBL; AY084419; AAM60993.1; -; mRNA.
DR RefSeq; NP_001078677.1; NM_001085208.2. [Q8W1X2-1]
DR RefSeq; NP_001331291.1; NM_001344222.1. [Q8W1X2-1]
DR RefSeq; NP_198601.2; NM_123144.4. [Q8W1X2-2]
DR AlphaFoldDB; Q8W1X2; -.
DR SMR; Q8W1X2; -.
DR BioGRID; 19014; 2.
DR STRING; 3702.AT5G37850.1; -.
DR iPTMnet; Q8W1X2; -.
DR PaxDb; Q8W1X2; -.
DR PRIDE; Q8W1X2; -.
DR ProteomicsDB; 236763; -. [Q8W1X2-1]
DR EnsemblPlants; AT5G37850.1; AT5G37850.1; AT5G37850. [Q8W1X2-2]
DR EnsemblPlants; AT5G37850.2; AT5G37850.2; AT5G37850. [Q8W1X2-1]
DR EnsemblPlants; AT5G37850.4; AT5G37850.4; AT5G37850. [Q8W1X2-1]
DR GeneID; 833763; -.
DR Gramene; AT5G37850.1; AT5G37850.1; AT5G37850. [Q8W1X2-2]
DR Gramene; AT5G37850.2; AT5G37850.2; AT5G37850. [Q8W1X2-1]
DR Gramene; AT5G37850.4; AT5G37850.4; AT5G37850. [Q8W1X2-1]
DR KEGG; ath:AT5G37850; -.
DR Araport; AT5G37850; -.
DR TAIR; locus:2153789; AT5G37850.
DR eggNOG; KOG2599; Eukaryota.
DR InParanoid; Q8W1X2; -.
DR OMA; CPNQLEL; -.
DR OrthoDB; 1091630at2759; -.
DR PhylomeDB; Q8W1X2; -.
DR BRENDA; 2.7.1.35; 399.
DR UniPathway; UPA01068; UER00298.
DR PRO; PR:Q8W1X2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q8W1X2; baseline and differential.
DR Genevisible; Q8W1X2; AT.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008478; F:pyridoxal kinase activity; IDA:TAIR.
DR GO; GO:0042538; P:hyperosmotic salinity response; IMP:TAIR.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009443; P:pyridoxal 5'-phosphate salvage; IDA:TAIR.
DR GO; GO:0008615; P:pyridoxine biosynthetic process; TAS:TAIR.
DR GO; GO:0010054; P:trichoblast differentiation; IMP:TAIR.
DR CDD; cd01173; pyridoxal_pyridoxamine_kinase; 1.
DR Gene3D; 3.40.1190.20; -; 1.
DR InterPro; IPR013749; PM/HMP-P_kinase-1.
DR InterPro; IPR004625; PyrdxlKinase.
DR InterPro; IPR029056; Ribokinase-like.
DR PANTHER; PTHR10534; PTHR10534; 1.
DR Pfam; PF08543; Phos_pyr_kin; 1.
DR SUPFAM; SSF53613; SSF53613; 1.
DR TIGRFAMs; TIGR00687; pyridox_kin; 1.
PE 1: Evidence at protein level;
KW Acetylation; Alternative splicing; ATP-binding; Direct protein sequencing;
KW Kinase; Magnesium; Metal-binding; Nucleotide-binding; Pyridoxal phosphate;
KW Reference proteome; Sodium; Transferase; Zinc.
FT CHAIN 1..309
FT /note="Pyridoxal kinase"
FT /id="PRO_0000213341"
FT INIT_MET 1
FT /note="Removed; alternate"
FT /evidence="ECO:0007744|PubMed:22223895"
FT CHAIN 2..309
FT /note="Pyridoxal kinase, N-terminally processed"
FT /id="PRO_0000434371"
FT ACT_SITE 234
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 23
FT /ligand="pyridoxal"
FT /ligand_id="ChEBI:CHEBI:17310"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 58
FT /ligand="pyridoxal"
FT /ligand_id="ChEBI:CHEBI:17310"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 58
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 124
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 124
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 129
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 155
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 157..160
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 193..194
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 193
FT /ligand="Na(+)"
FT /ligand_id="ChEBI:CHEBI:29101"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 225..227
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 232
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT BINDING 233..234
FT /ligand="pyridoxal 5'-phosphate"
FT /ligand_id="ChEBI:CHEBI:597326"
FT /evidence="ECO:0000250|UniProtKB:O00764"
FT MOD_RES 2
FT /note="N-acetylthreonine; in Pyridoxal kinase, N-terminally
FT processed"
FT /evidence="ECO:0007744|PubMed:22223895"
FT VAR_SEQ 1
FT /note="M -> MPFSFPTTTTTSLPFHKDHNHFNLNRNLRSRNRRM (in isoform
FT 2)"
FT /evidence="ECO:0000305"
FT /id="VSP_004654"
SQ SEQUENCE 309 AA; 34043 MW; 3630575692F2B271 CRC64;
MTTPPVLSLA LPSDTGRVLS IQSHTVQGYV GNKSAVFPLQ LLGYDVDPIN SVQFSNHTGY
PTFKGQVLNG QQLCDLIEGL EANDLLFYTH VLTGYIGSVS FLDTILEVIN KLRSVNPNLT
YVCDPVMGDE GKLYVPEELV HVYREKVVPL ASMLTPNQFE AEKLTGLRIN SEEDGREACA
ILHAAGPSKV VITSITIGGI LLLIGSHQKE KGLKPEQFKI LIHKIPAYFT GTGDLMTALL
LGWSNKYPDN LDKAAELAVS TLQALLRRTL DDYKRAGYDP TSSSLEIRLI QSQEDIRNPK
VELKAERYS
