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Protein

Pyridoxal kinase PdxY

Gene

pdxY

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP in vivo, but shows very low activity compared to PdxK. Displays a low level of pyridoxine kinase activity when overexpressed, which is however not physiologically relevant.2 Publications

Catalytic activityi

ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.2 Publications

Cofactori

Mg2+UniRule annotation

Pathwayi: pyridoxal 5'-phosphate salvage

This protein is involved in step 1 of the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxal.1 Publication
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxal kinase PdxY (pdxY), Pyridoxine/pyridoxal/pyridoxamine kinase (pdxK)
This subpathway is part of the pathway pyridoxal 5'-phosphate salvage, which is itself part of Cofactor metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes pyridoxal 5'-phosphate from pyridoxal, the pathway pyridoxal 5'-phosphate salvage and in Cofactor metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei10 – 101Substrate1 Publication
Binding sitei112 – 1121ATPBy similarity
Binding sitei144 – 1441ATP; via carbonyl oxygenBy similarity
Binding sitei149 – 1491ATPBy similarity
Binding sitei182 – 1821ATPBy similarity
Binding sitei224 – 2241Substrate1 Publication

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi209 – 2124ATPBy similarity

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • identical protein binding Source: EcoCyc
  • magnesium ion binding Source: UniProtKB-HAMAP
  • pyridoxal kinase activity Source: EcoCyc

GO - Biological processi

  • pyridoxal 5'-phosphate salvage Source: EcoliWiki
  • pyridoxal metabolic process Source: EcoliWiki
  • vitamin B6 biosynthetic process Source: EcoliWiki
Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

ATP-binding, Magnesium, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:PDXY-MONOMER.
ECOL316407:JW1628-MONOMER.
MetaCyc:PDXY-MONOMER.
UniPathwayiUPA01068; UER00298.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal kinase PdxY1 Publication (EC:2.7.1.352 Publications)
Short name:
PL kinase1 Publication
Alternative name(s):
Pyridoxal kinase 21 Publication
Short name:
PL kinase 21 Publication
Gene namesi
Name:pdxY1 Publication
Synonyms:ydgS
Ordered Locus Names:b1636, JW1628
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG13940. pdxY.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
Complete GO annotation...

Pathology & Biotechi

Disruption phenotypei

Cells lacking this gene and cells lacking both pdxY and pdxK are not auxotrophs, meaning that the de novo pathway of PLP biosynthesis is functional. For PLP salvage, the pdxY single mutant can use both pyridoxine and pyridoxal, the pdxK single mutant can use pyridoxal but not pyridoxine, and the double mutant can no longer use both compounds.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 287287Pyridoxal kinase PdxYPRO_0000213345Add
BLAST

Proteomic databases

PaxDbiP77150.

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4263486. 7 interactions.
IntActiP77150. 2 interactions.
STRINGi511145.b1636.

Structurei

Secondary structure

1
287
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 96Combined sources
Beta strandi12 – 154Combined sources
Helixi19 – 2810Combined sources
Beta strandi32 – 4312Combined sources
Helixi45 – 473Combined sources
Beta strandi52 – 543Combined sources
Helixi57 – 6913Combined sources
Helixi73 – 753Combined sources
Beta strandi78 – 814Combined sources
Helixi87 – 10317Combined sources
Beta strandi108 – 1114Combined sources
Turni118 – 1203Combined sources
Helixi128 – 1347Combined sources
Helixi136 – 1394Combined sources
Beta strandi141 – 1433Combined sources
Helixi147 – 1548Combined sources
Helixi161 – 17313Combined sources
Beta strandi177 – 1815Combined sources
Helixi185 – 1873Combined sources
Beta strandi188 – 1903Combined sources
Beta strandi193 – 1997Combined sources
Beta strandi204 – 2107Combined sources
Helixi222 – 23514Combined sources
Helixi240 – 26021Combined sources
Turni268 – 2725Combined sources
Helixi273 – 2764Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TD2X-ray2.22A/B1-287[»]
1VI9X-ray1.96A/B/C/D2-287[»]
ProteinModelPortaliP77150.
SMRiP77150. Positions 1-287.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP77150.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni45 – 462Substrate1 Publication

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4107XGF. Bacteria.
COG2240. LUCA.
HOGENOMiHOG000258173.
InParanoidiP77150.
KOiK00868.
OMAiCPNQLEL.
OrthoDBiEOG69PQ1X.
PhylomeDBiP77150.

Family and domain databases

Gene3Di3.40.1190.20. 1 hit.
HAMAPiMF_01639. PdxY.
InterProiIPR013749. PM/HMP-P_kinase-1.
IPR004625. PyrdxlKinase.
IPR023685. Pyridoxal_kinase_PdxY.
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.

Sequencei

Sequence statusi: Complete.

P77150-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMKNILAIQS HVVYGHAGNS AAEFPMRRLG ANVWPLNTVQ FSNHTQYGKW
60 70 80 90 100
TGCVMPPSHL TEIVQGIAAI DKLHTCDAVL SGYLGSAEQG EHILGIVRQV
110 120 130 140 150
KAANPQAKYF CDPVMGHPEK GCIVAPGVAE FHVRHGLPAS DIIAPNLVEL
160 170 180 190 200
EILCEHAVNN VEEAVLAARE LIAQGPQIVL VKHLARAGYS RDRFEMLLVT
210 220 230 240 250
ADEAWHISRP LVDFGMRQPV GVGDVTSGLL LVKLLQGATL QEALEHVTAA
260 270 280
VYEIMVTTKA MQEYELQVVA AQDRIAKPEH YFSATKL
Length:287
Mass (Da):31,322
Last modified:January 15, 2008 - v3
Checksum:iCD131649887E559A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74708.1.
AP009048 Genomic DNA. Translation: BAA15397.1.
PIRiF64920.
RefSeqiNP_416153.1. NC_000913.3.

Genome annotation databases

EnsemblBacteriaiAAC74708; AAC74708; b1636.
BAA15397; BAA15397; BAA15397.
GeneIDi946162.
KEGGiecj:JW1628.
eco:b1636.
PATRICi32118574. VBIEscCol129921_1707.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U00096 Genomic DNA. Translation: AAC74708.1.
AP009048 Genomic DNA. Translation: BAA15397.1.
PIRiF64920.
RefSeqiNP_416153.1. NC_000913.3.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1TD2X-ray2.22A/B1-287[»]
1VI9X-ray1.96A/B/C/D2-287[»]
ProteinModelPortaliP77150.
SMRiP77150. Positions 1-287.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263486. 7 interactions.
IntActiP77150. 2 interactions.
STRINGi511145.b1636.

Proteomic databases

PaxDbiP77150.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC74708; AAC74708; b1636.
BAA15397; BAA15397; BAA15397.
GeneIDi946162.
KEGGiecj:JW1628.
eco:b1636.
PATRICi32118574. VBIEscCol129921_1707.

Organism-specific databases

EchoBASEiEB3699.
EcoGeneiEG13940. pdxY.

Phylogenomic databases

eggNOGiENOG4107XGF. Bacteria.
COG2240. LUCA.
HOGENOMiHOG000258173.
InParanoidiP77150.
KOiK00868.
OMAiCPNQLEL.
OrthoDBiEOG69PQ1X.
PhylomeDBiP77150.

Enzyme and pathway databases

UniPathwayiUPA01068; UER00298.
BioCyciEcoCyc:PDXY-MONOMER.
ECOL316407:JW1628-MONOMER.
MetaCyc:PDXY-MONOMER.

Miscellaneous databases

EvolutionaryTraceiP77150.
PROiP77150.

Family and domain databases

Gene3Di3.40.1190.20. 1 hit.
HAMAPiMF_01639. PdxY.
InterProiIPR013749. PM/HMP-P_kinase-1.
IPR004625. PyrdxlKinase.
IPR023685. Pyridoxal_kinase_PdxY.
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. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  3. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  4. "Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate biosynthesis in Escherichia coli K-12."
    Yang Y., Tsui H.C., Man T.K., Winkler M.E.
    J. Bacteriol. 180:1814-1821(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, DISRUPTION PHENOTYPE, PATHWAY.
    Strain: K12.
  5. "Expression, purification, and kinetic constants for human and Escherichia coli pyridoxal kinases."
    di Salvo M.L., Hunt S., Schirch V.
    Protein Expr. Purif. 36:300-306(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY.
  6. "Crystal structure of the PdxY protein from Escherichia coli."
    Safo M.K., Musayev F.N., Hunt S., di Salvo M.L., Scarsdale N., Schirch V.
    J. Bacteriol. 186:8074-8082(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.22 ANGSTROMS) IN COMPLEX WITH PYRIDOXAL, SUBUNIT.
  7. Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF 2-287.

Entry informationi

Entry nameiPDXY_ECOLI
AccessioniPrimary (citable) accession number: P77150
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 15, 2008
Last modified: May 11, 2016
This is version 131 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  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.