O00764 (PDXK_HUMAN) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Pyridoxal kinase
EC=2.7.1.35

Alternative name(s):
Pyridoxine kinase

Gene names

Name:	PDXK
Synonyms:	C21orf124, C21orf97, PKH, PNK
ORF Names:	PRED79

Organism

Homo sapiens (Human) [Reference proteome]

Taxonomic identifier

9606 [NCBI]

Taxonomic lineage

cellular organisms › Eukaryota › Opisthokonta › Metazoa › Eumetazoa › Bilateria › Deuterostomia › Chordata › Craniata › Vertebrata › Gnathostomata › Teleostomi › Euteleostomi › Sarcopterygii › Tetrapoda › Amniota › Mammalia › Theria › Eutheria › Euarchontoglires › Primates › Haplorrhini › Simiiformes › Catarrhini › Hominoidea › Hominidae › Homininae › Homo

Protein attributes

Sequence length	312 AA.
Sequence status	Complete.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	Required for synthesis of pyridoxal-5-phosphate from vitamin B6.
Catalytic activity	ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.
Cofactor	Divalent cations. Zinc is more efficient than magnesium.
Subunit structure	Homodimer Probable.
Subcellular location	Cytoplasm.
Tissue specificity	Ubiquitous. Isoform 3 is detected in adult testis and spermatozoa.
Sequence similarities	Belongs to the pyridoxine kinase family.
Biophysicochemical properties	pH dependence: Optimum pH is 5.5-6.0.

Ontologies

Keywords
Cellular component	Cytoplasm
Coding sequence diversity	Alternative splicing
Ligand	ATP-binding Metal-binding Nucleotide-binding Zinc
Molecular function	Kinase Transferase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	cell proliferation Inferred from direct assay PubMed 10930737. Source: UniProtKB pyridoxal 5'-phosphate salvage Inferred from electronic annotation. Source: InterPro pyridoxal phosphate biosynthetic process Inferred from direct assay Ref.5PubMed 17766369Ref.1. Source: UniProtKB vitamin B6 metabolic process Inferred by curator PubMed 17766369. Source: UniProtKB
Cellular_component	cytosol Inferred from direct assay PubMed 16780588. Source: UniProtKB nucleus Inferred from direct assay. Source: HPA
Molecular_function	ATP binding Inferred from direct assay PubMed 16600635PubMed 17766369. Source: UniProtKB lithium ion binding Inferred from direct assay PubMed 9252787. Source: UniProtKB magnesium ion binding Inferred from direct assay PubMed 17766369. Source: UniProtKB potassium ion binding Inferred from direct assay PubMed 17766369PubMed 9252787. Source: UniProtKB protein homodimerization activity Inferred from direct assay PubMed 16600635PubMed 17766369. Source: UniProtKB pyridoxal kinase activity Inferred from direct assay Ref.5PubMed 17766369Ref.1. Source: UniProtKB pyridoxal phosphate binding Inferred from direct assay PubMed 16600635. Source: UniProtKB sodium ion binding Inferred from direct assay PubMed 17766369PubMed 9252787. Source: UniProtKB zinc ion binding Inferred from direct assay Ref.5. Source: UniProtKB
Complete GO annotation...

Alternative products

This entry describes 3 isoforms produced by alternative splicing. [Align] [Select]

Isoform 1 (identifier: O00764-1)

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.

Isoform 2 (identifier: O00764-2)

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

Note: No experimental confirmation available.

Isoform 3 (identifier: O00764-3)

Also known as: PKH-T;

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

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 312

312

Pyridoxal kinase

PRO_0000213335

Regions

Nucleotide binding

186 – 187

2

ATP By similarity

Nucleotide binding

223 – 234

12

ATP By similarity

Sites

Binding site

12

1

Substrate By similarity

Binding site

47

1

Substrate By similarity

Binding site

127

1

Substrate By similarity

Binding site

235

1

Substrate By similarity

Amino acid modifications

Modified residue

1

1

N-acetylmethionine By similarity

Modified residue

59

1

Phosphoserine Ref.7

Modified residue

164

1

Phosphoserine Ref.7

Modified residue

213

1

Phosphoserine Ref.6 Ref.7

Modified residue

285

1

Phosphoserine Ref.6 Ref.7

Natural variations

Alternative sequence

1 – 73

73

Missing in isoform 3.

VSP_010671

Alternative sequence

83 – 110

28

Missing in isoform 2.

VSP_004653

Secondary structure

1

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312

Helix Strand Turn

Details...

Beta strand

6 – 17

12

Helix

21 – 30

10

Beta strand

34 – 45

12

Beta strand

54 – 56

3

Helix

59 – 71

13

Beta strand

78 – 82

5

Helix

88 – 104

17

Beta strand

109 – 112

4

Beta strand

117 – 119

3

Beta strand

120 – 123

4

Beta strand

125 – 128

4

Helix

132 – 138

7

Helix

141 – 143

3

Beta strand

145 – 147

3

Helix

151 – 158

8

Helix

165 – 178

14

Beta strand

181 – 185

5

Beta strand

198 – 207

10

Turn

210 – 212

3

Beta strand

215 – 224

10

Helix

233 – 247

15

Helix

252 – 277

26

Turn

286 – 289

4

Helix

294 – 296

3

Helix

297 – 301

5

Beta strand

310 – 312

3

Sequences

	Sequence		Length	Mass (Da)
	Isoform 1 [UniParc]. Last modified July 1, 1997. Version 1. Checksum: 2DBDCAB5D8640569	FASTA	312	35,102
	10 20 30 40 50 60 MEEECRVLSI QSHVIRGYVG NRAATFPLQV LGFEIDAVNS VQFSNHTGYA HWKGQVLNSD 70 80 90 100 110 120 ELQELYEGLR LNNMNKYDYV LTGYTRDKSF LAMVVDIVQE LKQQNPRLVY VCDPVLGDKW 130 140 150 160 170 180 DGEGSMYVPE DLLPVYKEKV VPLADIITPN QFEAELLSGR KIHSQEEALR VMDMLHSMGP 190 200 210 220 230 240 DTVVITSSDL PSPQGSNYLI VLGSQRRRNP AGSVVMERIR MDIRKVDAVF VGTGDLFAAM 250 260 270 280 290 300 LLAWTHKHPN NLKVACEKTV STLHHVLQRT IQCAKAQAGE GVRPSPMQLE LRMVQSKRDI 310 EDPEIVVQAT VL
	Isoform 2 [UniParc]. Checksum: B85FE3EFD5A6B55D	FASTA	284	31,808
	10 20 30 40 50 60 MEEECRVLSI QSHVIRGYVG NRAATFPLQV LGFEIDAVNS VQFSNHTGYA HWKGQVLNSD 70 80 90 100 110 120 ELQELYEGLR LNNMNKYDYV LTVCDPVLGD KWDGEGSMYV PEDLLPVYKE KVVPLADIIT 130 140 150 160 170 180 PNQFEAELLS GRKIHSQEEA LRVMDMLHSM GPDTVVITSS DLPSPQGSNY LIVLGSQRRR 190 200 210 220 230 240 NPAGSVVMER IRMDIRKVDA VFVGTGDLFA AMLLAWTHKH PNNLKVACEK TVSTLHHVLQ 250 260 270 280 RTIQCAKAQA GEGVRPSPMQ LELRMVQSKR DIEDPEIVVQ ATVL
	Isoform 3 (PKH-T) [UniParc]. Checksum: 588E6BECD72D9640	FASTA	239	26,827
	10 20 30 40 50 60 MNKYDYVLTG YTRDKSFLAM VVDIVQELKQ QNPRLVYVCD PVLGDKWDGE GSMYVPEDLL 70 80 90 100 110 120 PVYKEKVVPL ADIITPNQFE AELLSGRKIH SQEEALRVMD MLHSMGPDTV VITSSDLPSP 130 140 150 160 170 180 QGSNYLIVLG SQRRRNPAGS VVMERIRMDI RKVDAVFVGT GDLFAAMLLA WTHKHPNNLK 190 200 210 220 230 VACEKTVSTL HHVLQRTIQC AKAQAGEGVR PSPMQLELRM VQSKRDIEDP EIVVQATVL

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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, MASS SPECTROMETRY. Tissue: Cervix carcinoma.
[7]	"Large-scale proteomics analysis of the human kinome." Oppermann F.S., Gnad F., Olsen J.V., Hornberger R., Greff Z., Keri G., Mann M., Daub H. Mol. Cell. Proteomics 8:1751-1764(2009) [PubMed] [Europe PMC] [Abstract] Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-59; SER-164; SER-213 AND SER-285, MASS SPECTROMETRY.
[8]	"Initial characterization of the human central proteome." Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T., Bennett K.L., Superti-Furga G., Colinge J. BMC Syst. Biol. 5:17-17(2011) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

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.

IPI

IPI00013004.
IPI00216320.
IPI00418202.

RefSeq

NP_003672.1. NM_003681.4.

UniGene

Hs.284491.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
2AJP	X-ray	2.50	A/B	6-312	[»]
2F7K	X-ray	2.80	A/B	1-312	[»]
2YXT	X-ray	2.00	A/B	1-312	[»]
2YXU	X-ray	2.20	A/B	1-312	[»]
3FHX	X-ray	2.50	A/B	1-312	[»]
3FHY	X-ray	2.30	A/B	1-312	[»]
3KEU	X-ray	2.10	A/B	1-312	[»]
4EN4	X-ray	2.15	A/B	1-312	[»]
4EOH	X-ray	2.10	A/B	1-312	[»]

ProteinModelPortal

O00764.

ModBase

Search...

Protein-protein interaction databases

IntAct

O00764. 4 interactions.

MINT

MINT-5002166.

STRING

9606.ENSP00000291565.

PTM databases

PhosphoSite

O00764.

2D gel databases

REPRODUCTION-2DPAGE

IPI00013004.
O00764.

Proteomic databases

PaxDb

O00764.

PRIDE

O00764.

Protocols and materials databases

DNASU

8566.

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

Ensembl

ENST00000291565; ENSP00000291565; ENSG00000160209.
ENST00000468090; ENSP00000418359; ENSG00000160209.

GeneID

8566.

KEGG

hsa:8566.

UCSC

uc002zdm.4. human.
uc002zdn.4. human.

Organism-specific databases

CTD

8566.

GeneCards

GC21P045138.

HGNC

HGNC:8819. PDXK.

HPA

CAB033918.
HPA030196.
HPA030197.
HPA030198.

MIM

179020. gene.

neXtProt

NX_O00764.

PharmGKB

PA33162.

GenAtlas

Search...

Phylogenomic databases

eggNOG

COG2240.

HOGENOM

HOG000258174.

HOVERGEN

HBG000732.

InParanoid

O00764.

KO

K00868.

OMA

TVSAMQH.

PhylomeDB

O00764.

Enzyme and pathway databases

BRENDA

2.7.1.35. 2681.

Reactome

REACT_111217. Metabolism.

SABIO-RK

O00764.

Gene expression databases

ArrayExpress

O00764.

Bgee

O00764.

CleanEx

HS_PDXK.

Genevestigator

O00764.

GermOnline

ENSG00000160209. Homo sapiens.

Family and domain databases

InterPro

IPR011611. PfkB_dom.
IPR004625. PyrdxlP_synth_PyrdxlKinase.
[Graphical view]

PANTHER

PTHR10534. PTHR10534. 1 hit.

Pfam

PF00294. PfkB. 1 hit.
[Graphical view]

TIGRFAMs

TIGR00687. pyridox_kin. 1 hit.

ProtoNet

Search...

Other

ChEMBL

CHEMBL1075181.

ChiTaRS

PDXK. human.

DrugBank

DB00147. Pyridoxal.
DB00165. Pyridoxine.

EvolutionaryTrace

O00764.

GenomeRNAi

8566.

NextBio

32117.

SOURCE

Search...

Entry information

Entry name

PDXK_HUMAN

Accession

Primary (citable) accession number: O00764
Secondary accession number(s): Q7Z2Y0, Q9BS02

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 1, 1997
Last sequence update:	July 1, 1997
Last modified:	May 1, 2013
This is version 130 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Chordata Protein Annotation Program

Disclaimer

Any 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.