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Protein

Pyridoxal kinase PdxY

Gene

pdxY

Organism
Shigella boydii serotype 4 (strain Sb227)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Protein inferred from homologyi

Functioni

Pyridoxal kinase involved in the salvage pathway of pyridoxal 5'-phosphate (PLP). Catalyzes the phosphorylation of pyridoxal to PLP.UniRule annotation

Catalytic activityi

ATP + pyridoxal = ADP + pyridoxal 5'-phosphate.UniRule annotation

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.UniRule annotation
Proteins known to be involved in this subpathway in this organism are:
  1. Pyridoxal kinase PdxY (pdxY)
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 – 101SubstrateUniRule annotation
Binding sitei112 – 1121ATPUniRule annotation
Binding sitei144 – 1441ATP; via carbonyl oxygenUniRule annotation
Binding sitei149 – 1491ATPUniRule annotation
Binding sitei182 – 1821ATPUniRule annotation
Binding sitei224 – 2241SubstrateUniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi209 – 2124ATPUniRule annotation

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Kinase, Transferase

Keywords - Ligandi

ATP-binding, Magnesium, Nucleotide-binding

Enzyme and pathway databases

BioCyciSBOY300268:GJFL-1495-MONOMER.
UniPathwayiUPA01068; UER00298.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal kinase PdxYUniRule annotation (EC:2.7.1.35UniRule annotation)
Short name:
PL kinaseUniRule annotation
Gene namesi
Name:pdxYUniRule annotation
Ordered Locus Names:SBO_1498
OrganismiShigella boydii serotype 4 (strain Sb227)
Taxonomic identifieri300268 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
Proteomesi
  • UP000007067 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 287287Pyridoxal kinase PdxYPRO_0000269830Add
BLAST

Interactioni

Subunit structurei

Homodimer.UniRule annotation

Structurei

3D structure databases

ProteinModelPortaliQ320Z3.
SMRiQ320Z3. Positions 1-287.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni45 – 462SubstrateUniRule annotation

Sequence similaritiesi

Belongs to the pyridoxine kinase family. PdxY subfamily.UniRule annotation

Phylogenomic databases

HOGENOMiHOG000258173.
KOiK00868.
OMAiCPNQLEL.
OrthoDBiEOG69PQ1X.

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.

Q320Z3-1 [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
CP000036 Genomic DNA. Translation: ABB66115.1.

Genome annotation databases

EnsemblBacteriaiABB66115; ABB66115; SBO_1498.
KEGGisbo:SBO_1498.
PATRICi18682010. VBIShiBoy33460_1939.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP000036 Genomic DNA. Translation: ABB66115.1.

3D structure databases

ProteinModelPortaliQ320Z3.
SMRiQ320Z3. Positions 1-287.
ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiABB66115; ABB66115; SBO_1498.
KEGGisbo:SBO_1498.
PATRICi18682010. VBIShiBoy33460_1939.

Phylogenomic databases

HOGENOMiHOG000258173.
KOiK00868.
OMAiCPNQLEL.
OrthoDBiEOG69PQ1X.

Enzyme and pathway databases

UniPathwayiUPA01068; UER00298.
BioCyciSBOY300268:GJFL-1495-MONOMER.

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

  1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Sb227.

Entry informationi

Entry nameiPDXY_SHIBS
AccessioniPrimary (citable) accession number: Q320Z3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 9, 2007
Last sequence update: January 15, 2008
Last modified: May 11, 2016
This is version 67 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

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. 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.