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Protein

Pyridoxal kinase

Gene

PK

Organism
Arabidopsis thaliana (Mouse-ear cress)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

Catalytic activityi

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

Cofactori

Zn2+Note: Divalent metal cations. Zn(2+) >> Co(2+) > Mg(2+) > Mn(2+) > Ca2+.

Kineticsi

  1. KM=98 µM for ATP
  2. KM=688 µM for pyridoxal

Vmax=1.604 mmol/min/mg enzyme

pH dependencei

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

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei23 – 231SubstrateBy similarity
Binding sitei58 – 581SubstrateBy similarity
Binding sitei134 – 1341SubstrateBy similarity
Binding sitei234 – 2341SubstrateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi193 – 1942ATPBy similarity
Nucleotide bindingi221 – 23313ATPBy similarityAdd
BLAST

GO - Molecular functioni

  1. ATP binding Source: UniProtKB-KW
  2. metal ion binding Source: UniProtKB-KW
  3. pyridoxal kinase activity Source: TAIR

GO - Biological processi

  1. hyperosmotic salinity response Source: TAIR
  2. phosphorylation Source: GOC
  3. pyridoxal 5'-phosphate salvage Source: TAIR
  4. pyridoxine biosynthetic process Source: TAIR
  5. trichoblast differentiation Source: TAIR
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Pyridoxal phosphate, Zinc

Enzyme and pathway databases

BioCyciARA:GQT-1103-MONOMER.
ARA:GQT-2581-MONOMER.
ReactomeiREACT_187833. Vitamins B6 activation to pyridoxal phosphate.
UniPathwayiUPA00190; 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
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
ProteomesiUP000006548: Chromosome 5

Organism-specific databases

TAIRiAT5G37850.

Subcellular locationi

GO - Cellular componenti

  1. cytosol Source: TAIR
Complete GO annotation...

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 309309Pyridoxal kinasePRO_0000213341Add
BLAST

Proteomic databases

PaxDbiQ8W1X2.
PRIDEiQ8W1X2.

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

GenevestigatoriQ8W1X2.

Interactioni

Subunit structurei

Homodimer.

Protein-protein interaction databases

BioGridi19014. 1 interaction.

Structurei

3D structure databases

ProteinModelPortaliQ8W1X2.
SMRiQ8W1X2. Positions 17-305.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the pyridoxine kinase family.Curated

Phylogenomic databases

eggNOGiCOG2240.
HOGENOMiHOG000258174.
InParanoidiQ8W1X2.
KOiK00868.
OMAiVYQQKVV.
PhylomeDBiQ8W1X2.

Family and domain databases

Gene3Di3.40.1190.20. 1 hit.
InterProiIPR013749. PM/HMP-P_kinase-1.
IPR004625. PyrdxlP_synth_PyrdxlKinase.
IPR029056. Ribokinase-like.
[Graphical view]
PANTHERiPTHR10534. PTHR10534. 1 hit.
PfamiPF08543. Phos_pyr_kin. 1 hit.
[Graphical view]
SUPFAMiSSF53613. SSF53613. 1 hit.
TIGRFAMsiTIGR00687. pyridox_kin. 1 hit.

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. Align

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)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 11M → MPFSFPTTTTTSLPFHKDHN HFNLNRNLRSRNRRM in isoform 2. CuratedVSP_004654

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.
AY136333 mRNA. Translation: AAM96999.1.
BT008815 mRNA. Translation: AAP68254.1.
AY084419 mRNA. Translation: AAM60993.1.
RefSeqiNP_001078677.1. NM_001085208.1. [Q8W1X2-1]
NP_198601.2. NM_123144.3. [Q8W1X2-2]
UniGeneiAt.28304.

Genome annotation databases

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

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

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.
AY136333 mRNA. Translation: AAM96999.1.
BT008815 mRNA. Translation: AAP68254.1.
AY084419 mRNA. Translation: AAM60993.1.
RefSeqiNP_001078677.1. NM_001085208.1. [Q8W1X2-1]
NP_198601.2. NM_123144.3. [Q8W1X2-2]
UniGeneiAt.28304.

3D structure databases

ProteinModelPortaliQ8W1X2.
SMRiQ8W1X2. Positions 17-305.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi19014. 1 interaction.

Proteomic databases

PaxDbiQ8W1X2.
PRIDEiQ8W1X2.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Organism-specific databases

TAIRiAT5G37850.

Phylogenomic databases

eggNOGiCOG2240.
HOGENOMiHOG000258174.
InParanoidiQ8W1X2.
KOiK00868.
OMAiVYQQKVV.
PhylomeDBiQ8W1X2.

Enzyme and pathway databases

UniPathwayiUPA00190; UER00298.
BioCyciARA:GQT-1103-MONOMER.
ARA:GQT-2581-MONOMER.
ReactomeiREACT_187833. Vitamins B6 activation to pyridoxal phosphate.

Miscellaneous databases

PROiQ8W1X2.

Gene expression databases

GenevestigatoriQ8W1X2.

Family and domain databases

Gene3Di3.40.1190.20. 1 hit.
InterProiIPR013749. PM/HMP-P_kinase-1.
IPR004625. PyrdxlP_synth_PyrdxlKinase.
IPR029056. Ribokinase-like.
[Graphical view]
PANTHERiPTHR10534. PTHR10534. 1 hit.
PfamiPF08543. Phos_pyr_kin. 1 hit.
[Graphical view]
SUPFAMiSSF53613. SSF53613. 1 hit.
TIGRFAMsiTIGR00687. pyridox_kin. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning and characterization of Arabidopsis thaliana pyridoxal kinase."
    Lum H.-K., Kwok F., Lo S.C.L.
    Planta 215:870-879(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), PROTEIN SEQUENCE OF 1-12.
    Strain: cv. Columbia.
  2. "The Arabidopsis salt overly sensitive 4 mutants uncover a critical role for vitamin B6 in plant salt tolerance."
    Shi H., Xiong L., Stevenson B., Lu T., Zhu J.-K.
    Plant Cell 14:575-588(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] (ISOFORMS 1 AND 2).
    Strain: cv. Columbia.
  3. "Structural analysis of Arabidopsis thaliana chromosome 5. VI. Sequence features of the regions of 1,367,185 bp covered by 19 physically assigned P1 and TAC clones."
    Kotani H., Nakamura Y., Sato S., Asamizu E., Kaneko T., Miyajima N., Tabata S.
    DNA Res. 5:203-216(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Columbia.
  4. The Arabidopsis Information Resource (TAIR)
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: GENOME REANNOTATION.
    Strain: cv. Columbia.
  5. "Empirical analysis of transcriptional activity in the Arabidopsis genome."
    Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M., Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G., Liu S.X., Lam B., Sakano H., Wu T., Yu G.
    , Miranda M., Quach H.L., Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C., Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J., Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A., Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C., Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X., Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M., Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K., Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A., Ecker J.R.
    Science 302:842-846(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
    Strain: cv. Columbia.
  6. "Full-length cDNA from Arabidopsis thaliana."
    Brover V.V., Troukhan M.E., Alexandrov N.A., Lu Y.-P., Flavell R.B., Feldmann K.A.
    Submitted (MAR-2002) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
  7. "SOS4, a pyridoxal kinase gene, is required for root hair development in Arabidopsis."
    Shi H., Zhu J.-K.
    Plant Physiol. 129:585-593(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION.

Entry informationi

Entry nameiPDXK_ARATH
AccessioniPrimary (citable) accession number: Q8W1X2
Secondary accession number(s): Q94EN4, Q9FKE1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 6, 2002
Last sequence update: December 6, 2002
Last modified: January 7, 2015
This is version 105 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

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

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Arabidopsis thaliana
    Arabidopsis thaliana: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.