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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)DescriptionActionsGraphical viewLength
Binding sitei10Substrate1 Publication1
Binding sitei112ATPBy similarity1
Binding sitei144ATP; via carbonyl oxygenBy similarity1
Binding sitei149ATPBy similarity1
Binding sitei182ATPBy similarity1
Binding sitei224Substrate1 Publication1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi209 – 212ATPBy similarity4

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
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)DescriptionActionsGraphical viewLength
ChainiPRO_00002133451 – 287Pyridoxal kinase PdxYAdd BLAST287

Proteomic databases

PaxDbiP77150.
PRIDEiP77150.

Interactioni

Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4263486. 7 interactors.
IntActiP77150. 2 interactors.
STRINGi511145.b1636.

Structurei

Secondary structure

1287
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi4 – 9Combined sources6
Beta strandi12 – 15Combined sources4
Helixi19 – 28Combined sources10
Beta strandi32 – 43Combined sources12
Helixi45 – 47Combined sources3
Beta strandi52 – 54Combined sources3
Helixi57 – 69Combined sources13
Helixi73 – 75Combined sources3
Beta strandi78 – 81Combined sources4
Helixi87 – 103Combined sources17
Beta strandi108 – 111Combined sources4
Turni118 – 120Combined sources3
Helixi128 – 134Combined sources7
Helixi136 – 139Combined sources4
Beta strandi141 – 143Combined sources3
Helixi147 – 154Combined sources8
Helixi161 – 173Combined sources13
Beta strandi177 – 181Combined sources5
Helixi185 – 187Combined sources3
Beta strandi188 – 190Combined sources3
Beta strandi193 – 199Combined sources7
Beta strandi204 – 210Combined sources7
Helixi222 – 235Combined sources14
Helixi240 – 260Combined sources21
Turni268 – 272Combined sources5
Helixi273 – 276Combined sources4

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP77150.

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni45 – 46Substrate1 Publication2

Sequence similaritiesi

Phylogenomic databases

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

Family and domain databases

CDDicd01173. pyridoxal_pyridoxamine_kinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
HAMAPiMF_01639. PdxY. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1TD2X-ray2.22A/B1-287[»]
1VI9X-ray1.96A/B/C/D2-287[»]
ProteinModelPortaliP77150.
SMRiP77150.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4263486. 7 interactors.
IntActiP77150. 2 interactors.
STRINGi511145.b1636.

Proteomic databases

PaxDbiP77150.
PRIDEiP77150.

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.
PhylomeDBiP77150.

Enzyme and pathway databases

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

Miscellaneous databases

EvolutionaryTraceiP77150.
PROiP77150.

Family and domain databases

CDDicd01173. pyridoxal_pyridoxamine_kinase. 1 hit.
Gene3Di3.40.1190.20. 1 hit.
HAMAPiMF_01639. PdxY. 1 hit.
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...

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: November 2, 2016
This is version 134 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.