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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

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the ‘correct annotation’ for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the ‘protein existence’ evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>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

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">Function</a> section describes the catalytic activity of an enzyme, i.e. a chemical reaction that the enzyme catalyzes.<p><a href='/help/catalytic_activity' target='_top'>More...</a></p>Catalytic activityi

<p>This subsection of the ‘Function’ section provides information relevant to cofactors. A cofactor is any non-protein substance required for a protein to be catalytically active. Some cofactors are inorganic, such as the metal atoms zinc, iron, and copper in various oxidation states. Others, such as most vitamins, are organic.<p><a href='/help/cofactor' target='_top'>More...</a></p>Cofactori

Mg2+UniRule annotation

<p>This subsection of the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section describes the metabolic pathway(s) associated with a protein.<p><a href='/help/pathway' target='_top'>More...</a></p>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
<p>This subsection of the ‘Function’ section describes the interaction between a single amino acid and another chemical entity. Priority is given to the annotation of physiological ligands.<p><a href='/help/binding' target='_top'>More...</a></p>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
<p>This subsection of the ‘Function’ section describes a region in the protein which binds nucleotide phosphates. It always involves more than one amino acid and includes all residues involved in nucleotide-binding.<p><a href='/help/np_bind' target='_top'>More...</a></p>Nucleotide bindingi209 – 212ATPBy similarity4

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

  • ATP binding Source: UniProtKB-UniRule
  • identical protein binding Source: EcoCyc
  • magnesium ion binding Source: UniProtKB-UniRule
  • 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

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionKinase, Transferase
LigandATP-binding, Magnesium, Nucleotide-binding

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:PDXY-MONOMER
MetaCyc:PDXY-MONOMER

UniPathway: a resource for the exploration and annotation of metabolic pathways

More...
UniPathwayi
UPA01068;UER00298

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>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
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: ‘Name’, ‘Synonyms’, ‘Ordered locus names’ and ‘ORF names’.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:pdxY1 Publication
Synonyms:ydgS
Ordered Locus Names:b1636, JW1628
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiEscherichia coli (strain K12)
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the ‘taxonomic identifier’ or ‘taxid’.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri83333 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000000318 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components. <br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

Escherichia coli strain K12 genome database

More...
EcoGenei
EG13940 pdxY

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

GO - Cellular componenti

<p>This section provides information on the disease(s) and phenotype(s) associated with a protein.<p><a href='/help/pathology_and_biotech_section' target='_top'>More...</a></p>Pathology & Biotechi

<p>This subsection of the ‘Pathology and Biotech’ section describes the in vivo effects caused by ablation of the gene (or one or more transcripts) coding for the protein described in the entry. This includes gene knockout and knockdown, provided experiments have been performed in the context of a whole organism or a specific tissue, and not at the single-cell level.<p><a href='/help/disruption_phenotype' target='_top'>More...</a></p>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

Chemistry databases

Drug and drug target database

More...
DrugBanki
DB02153 3-Sulfinoalanine

<p>This section describes post-translational modifications (PTMs) and/or processing events.<p><a href='/help/ptm_processing_section' target='_top'>More...</a></p>PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section describes the extent of a polypeptide chain in the mature protein following processing.<p><a href='/help/chain' target='_top'>More...</a></p>ChainiPRO_00002133451 – 287Pyridoxal kinase PdxYAdd BLAST287

Proteomic databases

PaxDb, a database of protein abundance averages across all three domains of life

More...
PaxDbi
P77150

PRoteomics IDEntifications database

More...
PRIDEi
P77150

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

Homodimer.1 Publication

GO - Molecular functioni

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4263486, 7 interactors

Protein interaction database and analysis system

More...
IntActi
P77150, 2 interactors

STRING: functional protein association networks

More...
STRINGi
316385.ECDH10B_1770

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

Secondary structure

1287
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

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ProteinModelPortali
P77150

SWISS-MODEL Repository - a database of annotated 3D protein structure models

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SMRi
P77150

Database of comparative protein structure models

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ModBasei
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P77150

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘Family and Domains’ section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni45 – 46Substrate1 Publication2

<p>This subsection of the ‘Family and domains’ section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4107XGF Bacteria
COG2240 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000258173

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P77150

KEGG Orthology (KO)

More...
KOi
K00868

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P77150

Family and domain databases

Conserved Domains Database

More...
CDDi
cd01173 pyridoxal_pyridoxamine_kinase, 1 hit

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.40.1190.20, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_01639 PdxY, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR013749 PM/HMP-P_kinase-1
IPR004625 PyrdxlKinase
IPR023685 Pyridoxal_kinase_PdxY
IPR029056 Ribokinase-like

The PANTHER Classification System

More...
PANTHERi
PTHR10534 PTHR10534, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF08543 Phos_pyr_kin, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF53613 SSF53613, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00687 pyridox_kin, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>.<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>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
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:iCD131649887E559A
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U00096 Genomic DNA Translation: AAC74708.1
AP009048 Genomic DNA Translation: BAA15397.1

Protein sequence database of the Protein Information Resource

More...
PIRi
F64920

NCBI Reference Sequences

More...
RefSeqi
NP_416153.1, NC_000913.3
WP_001307229.1, NZ_LN832404.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC74708; AAC74708; b1636
BAA15397; BAA15397; BAA15397

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
946162

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW1628
eco:b1636

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|511145.12.peg.1707

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>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
WP_001307229.1, NZ_LN832404.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
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
STRINGi316385.ECDH10B_1770

Chemistry databases

DrugBankiDB02153 3-Sulfinoalanine

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
PATRICifig|511145.12.peg.1707

Organism-specific databases

EchoBASE - an integrated post-genomic database for E. coli

More...
EchoBASEi
EB3699
EcoGeneiEG13940 pdxY

Phylogenomic databases

eggNOGiENOG4107XGF Bacteria
COG2240 LUCA
HOGENOMiHOG000258173
InParanoidiP77150
KOiK00868
PhylomeDBiP77150

Enzyme and pathway databases

UniPathwayi
UPA01068;UER00298

BioCyciEcoCyc:PDXY-MONOMER
MetaCyc:PDXY-MONOMER

Miscellaneous databases

EvolutionaryTraceiP77150

Protein Ontology

More...
PROi
PR:P77150

Family and domain databases

CDDicd01173 pyridoxal_pyridoxamine_kinase, 1 hit
Gene3Di3.40.1190.20, 1 hit
HAMAPiMF_01639 PdxY, 1 hit
InterProiView protein in InterPro
IPR013749 PM/HMP-P_kinase-1
IPR004625 PyrdxlKinase
IPR023685 Pyridoxal_kinase_PdxY
IPR029056 Ribokinase-like
PANTHERiPTHR10534 PTHR10534, 1 hit
PfamiView protein in Pfam
PF08543 Phos_pyr_kin, 1 hit
SUPFAMiSSF53613 SSF53613, 1 hit
TIGRFAMsiTIGR00687 pyridox_kin, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the ‘Entry information’ section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiPDXY_ECOLI
<p>This subsection of the ‘Entry information’ section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called ‘Primary (citable) accession number’.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: P77150
<p>This subsection of the ‘Entry information’ section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification (‘Last modified’). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: January 15, 2008
Last modified: December 5, 2018
This is version 143 of the entry and version 3 of the sequence. See complete history.
<p>This subsection of the ‘Entry information’ section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

<p>This section contains any relevant information that doesn’t fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  2. SIMILARITY comments
    Index of protein domains and families
  3. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  4. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
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