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Protein

Pyridoxal kinase

Gene

PDXK

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Required for synthesis of pyridoxal-5-phosphate from vitamin B6.

Catalytic activityi

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

Cofactori

Zn2+, Mg2+Note: Divalent metal cations. Zn2+ is more efficient than Mg2+.

pH dependencei

Optimum pH is 5.5-6.0.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei12SubstrateBy similarity1
Binding sitei47SubstrateBy similarity1
Binding sitei127SubstrateBy similarity1
Binding sitei235SubstrateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi186 – 187ATPBy similarity2
Nucleotide bindingi223 – 234ATPBy similarityAdd BLAST12

GO - Molecular functioni

  • ATP binding Source: UniProtKB
  • lithium ion binding Source: UniProtKB
  • magnesium ion binding Source: UniProtKB
  • potassium ion binding Source: UniProtKB
  • protein homodimerization activity Source: UniProtKB
  • pyridoxal kinase activity Source: UniProtKB
  • pyridoxal phosphate binding Source: UniProtKB
  • sodium ion binding Source: UniProtKB
  • zinc ion binding Source: UniProtKB

GO - Biological processi

  • cell proliferation Source: UniProtKB
  • pyridoxal 5'-phosphate salvage Source: GO_Central
  • pyridoxal phosphate biosynthetic process Source: UniProtKB
  • vitamin B6 metabolic process Source: UniProtKB
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

ATP-binding, Metal-binding, Nucleotide-binding, Zinc

Enzyme and pathway databases

BioCyciMetaCyc:HS08466-MONOMER.
ZFISH:HS08466-MONOMER.
BRENDAi2.7.1.35. 2681.
ReactomeiR-HSA-6798695. Neutrophil degranulation.
R-HSA-964975. Vitamins B6 activation to pyridoxal phosphate.
SABIO-RKO00764.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal kinase (EC:2.7.1.35)
Alternative name(s):
Pyridoxine kinase
Gene namesi
Name:PDXK
Synonyms:C21orf124, C21orf97, PKH, PNK
ORF Names:PRED79
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 21

Organism-specific databases

HGNCiHGNC:8819. PDXK.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: HPA
  • cytosol Source: UniProtKB
  • extracellular exosome Source: UniProtKB
  • nucleoplasm Source: HPA
  • nucleus Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi8566.
OpenTargetsiENSG00000160209.
PharmGKBiPA33162.

Chemistry databases

ChEMBLiCHEMBL1075181.
DrugBankiDB00147. Pyridoxal.
DB00165. Pyridoxine.

Polymorphism and mutation databases

BioMutaiPDXK.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002133351 – 312Pyridoxal kinaseAdd BLAST312

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei1N-acetylmethionineBy similarity1
Modified residuei59PhosphoserineCombined sources1
Modified residuei164PhosphoserineCombined sources1
Modified residuei213PhosphoserineCombined sources1
Modified residuei285PhosphoserineCombined sources1

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiO00764.
PaxDbiO00764.
PeptideAtlasiO00764.
PRIDEiO00764.

2D gel databases

REPRODUCTION-2DPAGEIPI00013004.
O00764.

PTM databases

iPTMnetiO00764.
PhosphoSitePlusiO00764.

Expressioni

Tissue specificityi

Ubiquitous. Isoform 3 is detected in adult testis and spermatozoa.

Gene expression databases

BgeeiENSG00000160209.
CleanExiHS_PDXK.
ExpressionAtlasiO00764. baseline and differential.
GenevisibleiO00764. HS.

Organism-specific databases

HPAiCAB033918.
HPA030196.
HPA030197.
HPA030198.

Interactioni

Subunit structurei

Homodimer.Curated

GO - Molecular functioni

  • protein homodimerization activity Source: UniProtKB

Protein-protein interaction databases

BioGridi114135. 23 interactors.
IntActiO00764. 5 interactors.
MINTiMINT-5002166.
STRINGi9606.ENSP00000291565.

Chemistry databases

BindingDBiO00764.

Structurei

Secondary structure

1312
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi6 – 17Combined sources12
Helixi21 – 30Combined sources10
Beta strandi34 – 45Combined sources12
Beta strandi54 – 56Combined sources3
Helixi59 – 71Combined sources13
Beta strandi78 – 82Combined sources5
Helixi88 – 104Combined sources17
Beta strandi109 – 112Combined sources4
Beta strandi117 – 119Combined sources3
Beta strandi120 – 123Combined sources4
Beta strandi125 – 128Combined sources4
Helixi132 – 138Combined sources7
Helixi141 – 143Combined sources3
Beta strandi145 – 147Combined sources3
Helixi151 – 158Combined sources8
Helixi165 – 178Combined sources14
Beta strandi181 – 185Combined sources5
Beta strandi198 – 208Combined sources11
Turni210 – 212Combined sources3
Beta strandi215 – 224Combined sources10
Helixi233 – 247Combined sources15
Helixi252 – 277Combined sources26
Turni286 – 289Combined sources4
Helixi294 – 296Combined sources3
Helixi297 – 301Combined sources5
Beta strandi310 – 312Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AJPX-ray2.50A/B6-312[»]
2F7KX-ray2.80A/B1-312[»]
2YXTX-ray2.00A/B1-312[»]
2YXUX-ray2.20A/B1-312[»]
3FHXX-ray2.50A/B1-312[»]
3FHYX-ray2.30A/B1-312[»]
3KEUX-ray2.10A/B1-312[»]
4EN4X-ray2.15A/B1-312[»]
4EOHX-ray2.10A/B1-312[»]
ProteinModelPortaliO00764.
SMRiO00764.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO00764.

Family & Domainsi

Sequence similaritiesi

Belongs to the pyridoxine kinase family.Curated

Phylogenomic databases

eggNOGiKOG2599. Eukaryota.
COG2240. LUCA.
GeneTreeiENSGT00390000003874.
HOGENOMiHOG000258174.
HOVERGENiHBG000732.
InParanoidiO00764.
KOiK00868.
OMAiVYQQKVV.
OrthoDBiEOG091G0EKE.
PhylomeDBiO00764.
TreeFamiTF315004.

Family and domain databases

CDDicd01173. pyridoxal_pyridoxamine_kinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
InterProiIPR013749. PM/HMP-P_kinase-1.
IPR004625. 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 (3)i

Sequence statusi: Complete.

This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: O00764-1) [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
MEEECRVLSI QSHVIRGYVG NRAATFPLQV LGFEIDAVNS VQFSNHTGYA
60 70 80 90 100
HWKGQVLNSD ELQELYEGLR LNNMNKYDYV LTGYTRDKSF LAMVVDIVQE
110 120 130 140 150
LKQQNPRLVY VCDPVLGDKW DGEGSMYVPE DLLPVYKEKV VPLADIITPN
160 170 180 190 200
QFEAELLSGR KIHSQEEALR VMDMLHSMGP DTVVITSSDL PSPQGSNYLI
210 220 230 240 250
VLGSQRRRNP AGSVVMERIR MDIRKVDAVF VGTGDLFAAM LLAWTHKHPN
260 270 280 290 300
NLKVACEKTV STLHHVLQRT IQCAKAQAGE GVRPSPMQLE LRMVQSKRDI
310
EDPEIVVQAT VL
Length:312
Mass (Da):35,102
Last modified:July 1, 1997 - v1
Checksum:i2DBDCAB5D8640569
GO
Isoform 2 (identifier: O00764-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     83-110: Missing.

Note: No experimental confirmation available.
Show »
Length:284
Mass (Da):31,808
Checksum:iB85FE3EFD5A6B55D
GO
Isoform 3 (identifier: O00764-3) [UniParc]FASTAAdd to basket
Also known as: PKH-T

The sequence of this isoform differs from the canonical sequence as follows:
     1-73: Missing.

Show »
Length:239
Mass (Da):26,827
Checksum:i588E6BECD72D9640
GO

Alternative sequence

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Alternative sequenceiVSP_0106711 – 73Missing in isoform 3. 1 PublicationAdd BLAST73
Alternative sequenceiVSP_00465383 – 110Missing in isoform 2. 1 PublicationAdd BLAST28

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89606 mRNA. Translation: AAC51233.1.
AY303972 mRNA. Translation: AAP73047.1.
AP001752 Genomic DNA. Translation: BAA95540.1.
BC000123 mRNA. Translation: AAH00123.1.
BC005825 mRNA. Translation: AAH05825.1.
CCDSiCCDS13699.1. [O00764-1]
RefSeqiNP_003672.1. NM_003681.4. [O00764-1]
XP_005261256.1. XM_005261199.2. [O00764-3]
XP_011528062.1. XM_011529760.2. [O00764-3]
XP_011528063.1. XM_011529761.1. [O00764-3]
XP_016883972.1. XM_017028483.1. [O00764-3]
XP_016883973.1. XM_017028484.1. [O00764-3]
UniGeneiHs.284491.

Genome annotation databases

EnsembliENST00000291565; ENSP00000291565; ENSG00000160209. [O00764-1]
ENST00000468090; ENSP00000418359; ENSG00000160209. [O00764-2]
GeneIDi8566.
KEGGihsa:8566.
UCSCiuc002zdn.4. human. [O00764-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U89606 mRNA. Translation: AAC51233.1.
AY303972 mRNA. Translation: AAP73047.1.
AP001752 Genomic DNA. Translation: BAA95540.1.
BC000123 mRNA. Translation: AAH00123.1.
BC005825 mRNA. Translation: AAH05825.1.
CCDSiCCDS13699.1. [O00764-1]
RefSeqiNP_003672.1. NM_003681.4. [O00764-1]
XP_005261256.1. XM_005261199.2. [O00764-3]
XP_011528062.1. XM_011529760.2. [O00764-3]
XP_011528063.1. XM_011529761.1. [O00764-3]
XP_016883972.1. XM_017028483.1. [O00764-3]
XP_016883973.1. XM_017028484.1. [O00764-3]
UniGeneiHs.284491.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2AJPX-ray2.50A/B6-312[»]
2F7KX-ray2.80A/B1-312[»]
2YXTX-ray2.00A/B1-312[»]
2YXUX-ray2.20A/B1-312[»]
3FHXX-ray2.50A/B1-312[»]
3FHYX-ray2.30A/B1-312[»]
3KEUX-ray2.10A/B1-312[»]
4EN4X-ray2.15A/B1-312[»]
4EOHX-ray2.10A/B1-312[»]
ProteinModelPortaliO00764.
SMRiO00764.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114135. 23 interactors.
IntActiO00764. 5 interactors.
MINTiMINT-5002166.
STRINGi9606.ENSP00000291565.

Chemistry databases

BindingDBiO00764.
ChEMBLiCHEMBL1075181.
DrugBankiDB00147. Pyridoxal.
DB00165. Pyridoxine.

PTM databases

iPTMnetiO00764.
PhosphoSitePlusiO00764.

Polymorphism and mutation databases

BioMutaiPDXK.

2D gel databases

REPRODUCTION-2DPAGEIPI00013004.
O00764.

Proteomic databases

EPDiO00764.
PaxDbiO00764.
PeptideAtlasiO00764.
PRIDEiO00764.

Protocols and materials databases

DNASUi8566.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000291565; ENSP00000291565; ENSG00000160209. [O00764-1]
ENST00000468090; ENSP00000418359; ENSG00000160209. [O00764-2]
GeneIDi8566.
KEGGihsa:8566.
UCSCiuc002zdn.4. human. [O00764-1]

Organism-specific databases

CTDi8566.
DisGeNETi8566.
GeneCardsiPDXK.
HGNCiHGNC:8819. PDXK.
HPAiCAB033918.
HPA030196.
HPA030197.
HPA030198.
MIMi179020. gene.
neXtProtiNX_O00764.
OpenTargetsiENSG00000160209.
PharmGKBiPA33162.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG2599. Eukaryota.
COG2240. LUCA.
GeneTreeiENSGT00390000003874.
HOGENOMiHOG000258174.
HOVERGENiHBG000732.
InParanoidiO00764.
KOiK00868.
OMAiVYQQKVV.
OrthoDBiEOG091G0EKE.
PhylomeDBiO00764.
TreeFamiTF315004.

Enzyme and pathway databases

BioCyciMetaCyc:HS08466-MONOMER.
ZFISH:HS08466-MONOMER.
BRENDAi2.7.1.35. 2681.
ReactomeiR-HSA-6798695. Neutrophil degranulation.
R-HSA-964975. Vitamins B6 activation to pyridoxal phosphate.
SABIO-RKO00764.

Miscellaneous databases

ChiTaRSiPDXK. human.
EvolutionaryTraceiO00764.
GeneWikiiPDXK.
GenomeRNAii8566.
PROiO00764.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000160209.
CleanExiHS_PDXK.
ExpressionAtlasiO00764. baseline and differential.
GenevisibleiO00764. HS.

Family and domain databases

CDDicd01173. pyridoxal_pyridoxamine_kinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
InterProiIPR013749. PM/HMP-P_kinase-1.
IPR004625. 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...

Entry informationi

Entry nameiPDXK_HUMAN
AccessioniPrimary (citable) accession number: O00764
Secondary accession number(s): Q7Z2Y0, Q9BS02
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 1, 1997
Last modified: November 30, 2016
This is version 166 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 21
    Human chromosome 21: entries, gene names and cross-references to MIM
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

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 one 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.