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Protein

Pyridoxal kinase

Gene

PDXK

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: -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

GO - Biological processi

Keywordsi

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

Enzyme and pathway databases

BioCyciMetaCyc:HS08466-MONOMER
BRENDAi2.7.1.35 2681
ReactomeiR-HSA-6798695 Neutrophil degranulation
R-HSA-964975 Vitamins B6 activation to pyridoxal phosphate
SABIO-RKiO00764

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

EuPathDBiHostDB:ENSG00000160209.18
HGNCiHGNC:8819 PDXK
MIMi179020 gene
neXtProtiNX_O00764

Subcellular locationi

Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Organism-specific databases

DisGeNETi8566
OpenTargetsiENSG00000160209
PharmGKBiPA33162

Chemistry databases

ChEMBLiCHEMBL1075181
DrugBankiDB04776 (2R)-2-({6-[benzyl(methyl)amino]-9-isopropyl-9H-purin-2-yl}amino)butan-1-ol
DB00147 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
ProteomicsDBi48024
48025 [O00764-2]
48026 [O00764-3]

2D gel databases

REPRODUCTION-2DPAGEiIPI00013004
O00764

PTM databases

iPTMnetiO00764
PhosphoSitePlusiO00764

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiENSG00000160209 Expressed in 228 organ(s), highest expression level in right testis
CleanExiHS_PDXK
ExpressionAtlasiO00764 baseline and differential
GenevisibleiO00764 HS

Organism-specific databases

HPAiCAB033918
HPA030196
HPA030197
HPA030198

Interactioni

Subunit structurei

Homodimer.Curated

GO - Molecular functioni

Protein-protein interaction databases

BioGridi114135, 26 interactors
CORUMiO00764
IntActiO00764, 5 interactors
MINTiO00764
STRINGi9606.ENSP00000291565

Chemistry databases

BindingDBiO00764

Structurei

Secondary structure

1312
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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
OMAiCPNQLEL
OrthoDBiEOG091G0EKE
PhylomeDBiO00764
TreeFamiTF315004

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 (3+)i

Sequence statusi: Complete.

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

This entry has 3 described isoforms and 4 potential isoforms that are computationally mapped.Show allAlign All

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

Computationally mapped potential isoform sequencesi

There are 4 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basket
EntryEntry nameProtein names
Gene namesLengthAnnotation
F2Z2Y4F2Z2Y4_HUMAN
Pyridoxal kinase
PDXK
272Annotation score:
A8MV33A8MV33_HUMAN
HCG401289, isoform CRA_b
PDXK hCG_401289
87Annotation score:
A0A0B4J2C9A0A0B4J2C9_HUMAN
Pyridoxal kinase
PDXK
162Annotation score:
A8MT14A8MT14_HUMAN
HCG401289, isoform CRA_e
PDXK hCG_401289
148Annotation score:

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

Similar proteinsi

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, 26 interactors
CORUMiO00764
IntActiO00764, 5 interactors
MINTiO00764
STRINGi9606.ENSP00000291565

Chemistry databases

BindingDBiO00764
ChEMBLiCHEMBL1075181
DrugBankiDB04776 (2R)-2-({6-[benzyl(methyl)amino]-9-isopropyl-9H-purin-2-yl}amino)butan-1-ol
DB00147 Pyridoxal
DB00165 Pyridoxine

PTM databases

iPTMnetiO00764
PhosphoSitePlusiO00764

Polymorphism and mutation databases

BioMutaiPDXK

2D gel databases

REPRODUCTION-2DPAGEiIPI00013004
O00764

Proteomic databases

EPDiO00764
PaxDbiO00764
PeptideAtlasiO00764
PRIDEiO00764
ProteomicsDBi48024
48025 [O00764-2]
48026 [O00764-3]

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
EuPathDBiHostDB:ENSG00000160209.18
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
OMAiCPNQLEL
OrthoDBiEOG091G0EKE
PhylomeDBiO00764
TreeFamiTF315004

Enzyme and pathway databases

BioCyciMetaCyc:HS08466-MONOMER
BRENDAi2.7.1.35 2681
ReactomeiR-HSA-6798695 Neutrophil degranulation
R-HSA-964975 Vitamins B6 activation to pyridoxal phosphate
SABIO-RKiO00764

Miscellaneous databases

ChiTaRSiPDXK human
EvolutionaryTraceiO00764
GeneWikiiPDXK
GenomeRNAii8566
PROiPR:O00764
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000160209 Expressed in 228 organ(s), highest expression level in right testis
CleanExiHS_PDXK
ExpressionAtlasiO00764 baseline and differential
GenevisibleiO00764 HS

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
ProtoNetiSearch...

Entry informationi

Entry nameiPDXK_HUMAN
AccessioniPrimary (citable) accession number: O00764
Secondary accession number(s): Q7Z2Y0, Q9BS02
Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: July 1, 1997
Last modified: October 10, 2018
This is version 180 of the entry and version 1 of the sequence. See 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. SIMILARITY comments
    Index of protein domains and families
  2. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  3. Human chromosome 21
    Human chromosome 21: entries, gene names and cross-references to MIM
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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