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Protein

Pyridoxal kinase

Gene

PK

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the transfer of a phosphate group from ATP to the 5-hydroxylmethyl group of pyridoxal to form the biologically active pyridoxal phosphate.1 Publication

Miscellaneous

Defective pyridoxal kinase results in both salt hypersensitive and root hairless phenotypes.

Catalytic activityi

ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.

Cofactori

Zn2+Note: Divalent metal cations. Zn2+ >> Co2+ > Mg2+ > Mn2+ > Ca2+.

Kineticsi

  1. KM=98 µM for ATP
  2. KM=688 µM for pyridoxal
  1. Vmax=1.604 mmol/min/mg enzyme

pH dependencei

Optimum pH is 6.0. Active from pH 4.5 to 10.5.

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxal.
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxal kinase (PK)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxal, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei23SubstrateBy similarity1
Binding sitei58SubstrateBy similarity1
Binding sitei134SubstrateBy similarity1
Binding sitei234SubstrateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi193 – 194ATPBy similarity2
Nucleotide bindingi221 – 233ATPBy similarityAdd BLAST13

GO - Molecular functioni

  • ATP binding Source: UniProtKB-KW
  • metal ion binding Source: UniProtKB-KW
  • pyridoxal kinase activity Source: TAIR

GO - Biological processi

  • hyperosmotic salinity response Source: TAIR
  • pyridoxal 5'-phosphate salvage Source: TAIR
  • pyridoxine biosynthetic process Source: TAIR
  • trichoblast differentiation Source: TAIR

Keywordsi

Molecular functionKinase, Transferase
LigandATP-binding, Metal-binding, Nucleotide-binding, Pyridoxal phosphate, Zinc

Enzyme and pathway databases

BRENDAi2.7.1.35 399
ReactomeiR-ATH-6798695 Neutrophil degranulation
R-ATH-964975 Vitamins B6 activation to pyridoxal phosphate
UniPathwayiUPA01068; UER00298

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal kinase (EC:2.7.1.35)
Alternative name(s):
Protein SALT OVERLY SENSITIVE 4
Pyridoxal kinase-like protein SOS4
Pyridoxine kinase
Cleaved into the following chain:
Gene namesi
Name:PK
Synonyms:PDXK, SOS4
Ordered Locus Names:At5g37850
ORF Names:K18L3_10
OrganismiArabidopsis thaliana (Mouse-ear cress)
Taxonomic identifieri3702 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaeudicotyledonsGunneridaePentapetalaerosidsmalvidsBrassicalesBrassicaceaeCamelineaeArabidopsis
Proteomesi
  • UP000006548 Componenti: Chromosome 5

Organism-specific databases

AraportiAT5G37850
TAIRilocus:2153789 AT5G37850

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002133411 – 309Pyridoxal kinaseAdd BLAST309
Initiator methionineiRemoved; alternateCombined sources
ChainiPRO_00004343712 – 309Pyridoxal kinase, N-terminally processedAdd BLAST308

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei2N-acetylthreonine; in Pyridoxal kinase, N-terminally processedCombined sources1

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ8W1X2

PTM databases

iPTMnetiQ8W1X2

Expressioni

Tissue specificityi

Expressed ubiquitously in leaves, stems, roots, flowers and siliques.

Developmental stagei

Becomes detectable 60 hours after imbibition of the seeds and remains constant up to 101 hours after imbibition.

Inductioni

Both long and short transcripts are down-regulated in roots but not in shoots by NaCl and abscisic acid treatment. Under cold stress, the expression of the short transcript is increased while the long one becomes undetectable.

Gene expression databases

ExpressionAtlasiQ8W1X2 baseline and differential
GenevisibleiQ8W1X2 AT

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi19014, 2 interactors
STRINGi3702.AT5G37850.1

Structurei

3D structure databases

ProteinModelPortaliQ8W1X2
SMRiQ8W1X2
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the pyridoxine kinase family.Curated

Phylogenomic databases

eggNOGiKOG2599 Eukaryota
COG2240 LUCA
HOGENOMiHOG000258174
InParanoidiQ8W1X2
KOiK00868
OMAiCPNQLEL
OrthoDBiEOG09360HKF
PhylomeDBiQ8W1X2

Family and domain databases

CDDicd01173 pyridoxal_pyridoxamine_kinase, 1 hit
Gene3Di3.40.1190.20, 1 hit
InterProiView protein in InterPro
IPR013749 PM/HMP-P_kinase-1
IPR004625 PyrdxlKinase
IPR029056 Ribokinase-like
PANTHERiPTHR10534 PTHR10534, 1 hit
PfamiView protein in Pfam
PF08543 Phos_pyr_kin, 1 hit
SUPFAMiSSF53613 SSF53613, 1 hit
TIGRFAMsiTIGR00687 pyridox_kin, 1 hit

Sequences (2)i

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q8W1X2-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MTTPPVLSLA LPSDTGRVLS IQSHTVQGYV GNKSAVFPLQ LLGYDVDPIN
60 70 80 90 100
SVQFSNHTGY PTFKGQVLNG QQLCDLIEGL EANDLLFYTH VLTGYIGSVS
110 120 130 140 150
FLDTILEVIN KLRSVNPNLT YVCDPVMGDE GKLYVPEELV HVYREKVVPL
160 170 180 190 200
ASMLTPNQFE AEKLTGLRIN SEEDGREACA ILHAAGPSKV VITSITIGGI
210 220 230 240 250
LLLIGSHQKE KGLKPEQFKI LIHKIPAYFT GTGDLMTALL LGWSNKYPDN
260 270 280 290 300
LDKAAELAVS TLQALLRRTL DDYKRAGYDP TSSSLEIRLI QSQEDIRNPK

VELKAERYS
Length:309
Mass (Da):34,043
Last modified:December 6, 2002 - v2
Checksum:i3630575692F2B271
GO
Isoform 2 (identifier: Q8W1X2-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-1: M → MPFSFPTTTTTSLPFHKDHNHFNLNRNLRSRNRRM

Note: No experimental confirmation available.
Show »
Length:343
Mass (Da):38,167
Checksum:i58DFE7EF6334C178
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0046541M → MPFSFPTTTTTSLPFHKDHN HFNLNRNLRSRNRRM in isoform 2. Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF404865 mRNA Translation: AAL57364.2
AF400125 Genomic DNA Translation: AAK94020.1
AF400125 Genomic DNA Translation: AAK94021.1
AB012241 Genomic DNA Translation: BAB09031.1
CP002688 Genomic DNA Translation: AED94239.1
CP002688 Genomic DNA Translation: AED94240.1
CP002688 Genomic DNA Translation: ANM69628.1
AY136333 mRNA Translation: AAM96999.1
BT008815 mRNA Translation: AAP68254.1
AY084419 mRNA Translation: AAM60993.1
RefSeqiNP_001078677.1, NM_001085208.2 [Q8W1X2-1]
NP_001331291.1, NM_001344222.1 [Q8W1X2-1]
NP_198601.2, NM_123144.4 [Q8W1X2-2]
UniGeneiAt.28304

Genome annotation databases

EnsemblPlantsiAT5G37850.1; AT5G37850.1; AT5G37850 [Q8W1X2-2]
AT5G37850.2; AT5G37850.2; AT5G37850 [Q8W1X2-1]
AT5G37850.4; AT5G37850.4; AT5G37850 [Q8W1X2-1]
GeneIDi833763
GrameneiAT5G37850.1; AT5G37850.1; AT5G37850 [Q8W1X2-2]
AT5G37850.2; AT5G37850.2; AT5G37850 [Q8W1X2-1]
AT5G37850.4; AT5G37850.4; AT5G37850 [Q8W1X2-1]
KEGGiath:AT5G37850

Keywords - Coding sequence diversityi

Alternative splicing

Similar proteinsi

Entry informationi

Entry nameiPDXK_ARATH
AccessioniPrimary (citable) accession number: Q8W1X2
Secondary accession number(s): Q94EN4, Q9FKE1
Entry historyiIntegrated into UniProtKB/Swiss-Prot: December 6, 2002
Last sequence update: December 6, 2002
Last modified: April 25, 2018
This is version 127 of the entry and version 2 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome
UniProt is an ELIXIR core data resource
Main funding by: National Institutes of Health