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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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121SubstrateBy similarity
Binding sitei47 – 471SubstrateBy similarity
Binding sitei127 – 1271SubstrateBy similarity
Binding sitei235 – 2351SubstrateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi186 – 1872ATPBy similarity
Nucleotide bindingi223 – 23412ATPBy similarityAdd
BLAST

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.
BRENDAi2.7.1.35. 2681.
ReactomeiR-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

PharmGKBiPA33162.

Chemistry

ChEMBLiCHEMBL1075181.
DrugBankiDB00147. Pyridoxal.
DB00165. Pyridoxine.

Polymorphism and mutation databases

BioMutaiPDXK.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 312312Pyridoxal kinasePRO_0000213335Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei1 – 11N-acetylmethionineBy similarity
Modified residuei59 – 591PhosphoserineCombined sources
Modified residuei164 – 1641PhosphoserineCombined sources
Modified residuei213 – 2131PhosphoserineCombined sources
Modified residuei285 – 2851PhosphoserineCombined sources

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

EPDiO00764.
PaxDbiO00764.
PRIDEiO00764.

2D gel databases

REPRODUCTION-2DPAGEIPI00013004.
O00764.

PTM databases

iPTMnetiO00764.
PhosphoSiteiO00764.

Expressioni

Tissue specificityi

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

Gene expression databases

BgeeiO00764.
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 interactions.
IntActiO00764. 5 interactions.
MINTiMINT-5002166.
STRINGi9606.ENSP00000291565.

Chemistry

BindingDBiO00764.

Structurei

Secondary structure

1
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi6 – 1712Combined sources
Helixi21 – 3010Combined sources
Beta strandi34 – 4512Combined sources
Beta strandi54 – 563Combined sources
Helixi59 – 7113Combined sources
Beta strandi78 – 825Combined sources
Helixi88 – 10417Combined sources
Beta strandi109 – 1124Combined sources
Beta strandi117 – 1193Combined sources
Beta strandi120 – 1234Combined sources
Beta strandi125 – 1284Combined sources
Helixi132 – 1387Combined sources
Helixi141 – 1433Combined sources
Beta strandi145 – 1473Combined sources
Helixi151 – 1588Combined sources
Helixi165 – 17814Combined sources
Beta strandi181 – 1855Combined sources
Beta strandi198 – 20811Combined sources
Turni210 – 2123Combined sources
Beta strandi215 – 22410Combined sources
Helixi233 – 24715Combined sources
Helixi252 – 27726Combined sources
Turni286 – 2894Combined sources
Helixi294 – 2963Combined sources
Helixi297 – 3015Combined sources
Beta strandi310 – 3123Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 3-312.
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.
OMAiRIRMEMH.
PhylomeDBiO00764.
TreeFamiTF315004.

Family and domain databases

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)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 7373Missing in isoform 3. 1 PublicationVSP_010671Add
BLAST
Alternative sequencei83 – 11028Missing in isoform 2. 1 PublicationVSP_004653Add
BLAST

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_011529760.1. [O00764-3]
XP_011528063.1. XM_011529761.1. [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_011529760.1. [O00764-3]
XP_011528063.1. XM_011529761.1. [O00764-3]
UniGeneiHs.284491.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
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. Positions 3-312.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

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

Chemistry

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

PTM databases

iPTMnetiO00764.
PhosphoSiteiO00764.

Polymorphism and mutation databases

BioMutaiPDXK.

2D gel databases

REPRODUCTION-2DPAGEIPI00013004.
O00764.

Proteomic databases

EPDiO00764.
PaxDbiO00764.
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.
GeneCardsiPDXK.
HGNCiHGNC:8819. PDXK.
HPAiCAB033918.
HPA030196.
HPA030197.
HPA030198.
MIMi179020. gene.
neXtProtiNX_O00764.
PharmGKBiPA33162.
GenAtlasiSearch...

Phylogenomic databases

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

Enzyme and pathway databases

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

Miscellaneous databases

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

Gene expression databases

BgeeiO00764.
CleanExiHS_PDXK.
ExpressionAtlasiO00764. baseline and differential.
GenevisibleiO00764. HS.

Family and domain databases

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...

Publicationsi

« Hide 'large scale' publications
  1. "Human pyridoxal kinase. cDNA cloning, expression, and modulation by ligands of the benzodiazepine receptor."
    Hanna M.C., Turner A.J., Kirkness E.F.
    J. Biol. Chem. 272:10756-10760(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  2. "Expression of a novel pyridoxal kinase mRNA splice variant, PKH-T, in human testis."
    Fang X., Zhou Z.M., Lu L., Yin L.L., Li J.M., Zhen Y., Wang H., Sha J.H.
    Asian J. Androl. 6:83-91(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 3).
    Tissue: Testis.
  3. "The DNA sequence of human chromosome 21."
    Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.-S., Toyoda A., Ishii K., Totoki Y., Choi D.-K., Groner Y., Soeda E., Ohki M., Takagi T., Sakaki Y., Taudien S., Blechschmidt K., Polley A.
    , Menzel U., Delabar J., Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., Schillhabel M., Schudy A., Zimmermann W., Rosenthal A., Kudoh J., Shibuya K., Kawasaki K., Asakawa S., Shintani A., Sasaki T., Nagamine K., Mitsuyama S., Antonarakis S.E., Minoshima S., Shimizu N., Nordsiek G., Hornischer K., Brandt P., Scharfe M., Schoen O., Desario A., Reichelt J., Kauer G., Bloecker H., Ramser J., Beck A., Klages S., Hennig S., Riesselmann L., Dagand E., Wehrmeyer S., Borzym K., Gardiner K., Nizetic D., Francis F., Lehrach H., Reinhardt R., Yaspo M.-L.
    Nature 405:311-319(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
    Tissue: Eye and Ovary.
  5. "Human pyridoxal kinase: overexpression and properties of the recombinant enzyme."
    Lee H.-S., Moon B.J., Choi S.Y., Kwon O.-S.
    Mol. Cells 10:452-459(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  6. "Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle."
    Daub H., Olsen J.V., Bairlein M., Gnad F., Oppermann F.S., Korner R., Greff Z., Keri G., Stemmann O., Mann M.
    Mol. Cell 31:438-448(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-213 AND SER-285, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Cervix carcinoma.
  7. Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59; SER-164; SER-213 AND SER-285, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  8. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  9. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.

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: June 8, 2016
This is version 161 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.