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Entry version 114 (13 Nov 2019)
Sequence version 1 (11 Oct 2004)
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Protein

Pyridoxal phosphate homeostasis protein

Gene

yggS

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score:

Annotation score:4 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 5'-phosphate (PLP)-binding protein, which is involved in PLP homeostasis. May have a carrier function to deliver PLP to the target enzymes or a protective function so that PLP does not inactivate essential lysines in proteins (PubMed:26872910). Does not have amino acid racemase activity (PubMed:24097949).2 Publications

<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

<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

LigandPyridoxal phosphate

Enzyme and pathway databases

BioCyc Collection of Pathway/Genome Databases

More...
BioCyci
EcoCyc:G7527-MONOMER
ECOL316407:JW2918-MONOMER

<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 phosphate homeostasis proteinUniRule annotationCurated
Short name:
PLP homeostasis proteinUniRule annotationCurated
<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:yggS
Ordered Locus Names:b2951, JW2918
<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

<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

During the stationary phase, the deletion mutant exhibits a completely different intracellular pool of amino acids and produces a significant amount of L-valine in the culture medium. The log-phase mutant displays slightly decreased coenzyme A levels, accumulates 2-ketobutyrate, 2-aminobutyrate, and, to a lesser extent, L-valine. Also exhibits an increase in the levels of isoleucine and valine metabolic enzymes (PubMed:24097949). The mutant also accumulates gamma-L-glutamyl-L-2-aminobutyryl-glycine (ophthalmic acid) (PubMed:27426274). The mutant accumulates the PLP precursor pyridoxine 5'-phosphate (PNP), and is sensitive to an excess of pyridoxine but not of pyridoxal (PubMed:26872910). Most of the phenotypes observed in the absence of yggS are probably caused by lower activities of PLP-dependent enzymes (PubMed:26872910).1 Publication3 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/manual/pathology_and_biotech_section">'Pathology and Biotech'</a> section describes the effect of the experimental mutation of one or more amino acid(s) on the biological properties of the protein.<p><a href='/help/mutagen' target='_top'>More...</a></p>Mutagenesisi36K → A: Does not bind PLP. 1 Publication1

<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_00001631961 – 234Pyridoxal phosphate homeostasis proteinAdd BLAST234

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the ‘PTM / Processing’ section specifies the position and type of each modified residue excluding <a href="http://www.uniprot.org/manual/lipid">lipids</a>, <a href="http://www.uniprot.org/manual/carbohyd">glycans</a> and <a href="http://www.uniprot.org/manual/crosslnk">protein cross-links</a>.<p><a href='/help/mod_res' target='_top'>More...</a></p>Modified residuei36N6-(pyridoxal phosphate)lysineUniRule annotationCombined sources1 Publication1

Proteomic databases

jPOST - Japan Proteome Standard Repository/Database

More...
jPOSTi
P67080

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

More...
PaxDbi
P67080

PRoteomics IDEntifications database

More...
PRIDEi
P67080

<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

Monomer.

UniRule annotation1 Publication

Protein-protein interaction databases

The Biological General Repository for Interaction Datasets (BioGrid)

More...
BioGridi
4261786, 34 interactors
851744, 1 interactor

Database of interacting proteins

More...
DIPi
DIP-12194N

Protein interaction database and analysis system

More...
IntActi
P67080, 9 interactors

STRING: functional protein association networks

More...
STRINGi
511145.b2951

<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

1234
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details

3D structure databases

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

More...
SMRi
P67080

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

Miscellaneous databases

Relative evolutionary importance of amino acids within a protein sequence

More...
EvolutionaryTracei
P67080

<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

<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

Belongs to the pyridoxal phosphate-binding protein YggS/PROSC family.UniRule annotationCurated

Phylogenomic databases

evolutionary genealogy of genes: Non-supervised Orthologous Groups

More...
eggNOGi
ENOG4105DFA Bacteria
COG0325 LUCA

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
HOG000048983

InParanoid: Eukaryotic Ortholog Groups

More...
InParanoidi
P67080

KEGG Orthology (KO)

More...
KOi
K06997

Database for complete collections of gene phylogenies

More...
PhylomeDBi
P67080

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
3.20.20.10, 1 hit

HAMAP database of protein families

More...
HAMAPi
MF_02087 PLP_homeostasis, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR001608 Ala_racemase_N
IPR029066 PLP-binding_barrel
IPR011078 PyrdxlP_homeostasis

The PANTHER Classification System

More...
PANTHERi
PTHR10146 PTHR10146, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF01168 Ala_racemase_N, 1 hit

PIRSF; a whole-protein classification database

More...
PIRSFi
PIRSF004848 YBL036c_PLPDEIII, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF51419 SSF51419, 1 hit

TIGRFAMs; a protein family database

More...
TIGRFAMsi
TIGR00044 TIGR00044, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS01211 UPF0001, 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>. The information is filed in different subsections. The current subsections and their content are listed below:<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.

P67080-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MNDIAHNLAQ VRDKISAAAT RCGRSPEEIT LLAVSKTKPA SAIAEAIDAG
60 70 80 90 100
QRQFGENYVQ EGVDKIRHFQ ELGVTGLEWH FIGPLQSNKS RLVAEHFDWC
110 120 130 140 150
HTIDRLRIAT RLNDQRPAEL PPLNVLIQIN ISDENSKSGI QLAELDELAA
160 170 180 190 200
AVAELPRLRL RGLMAIPAPE SEYVRQFEVA RQMAVAFAGL KTRYPHIDTL
210 220 230
SLGMSDDMEA AIAAGSTMVR IGTAIFGARD YSKK
Length:234
Mass (Da):25,787
Last modified:October 11, 2004 - v1
<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:i2AA431E2D75BCA59
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

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EMBLi

GenBank nucleotide sequence database

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GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
U28377 Genomic DNA Translation: AAA69118.1
U00096 Genomic DNA Translation: AAC75988.1
AP009048 Genomic DNA Translation: BAE77014.1

Protein sequence database of the Protein Information Resource

More...
PIRi
F65080

NCBI Reference Sequences

More...
RefSeqi
NP_417426.1, NC_000913.3
WP_000997795.1, NZ_STEB01000001.1

Genome annotation databases

Ensembl bacterial and archaeal genome annotation project

More...
EnsemblBacteriai
AAC75988; AAC75988; b2951
BAE77014; BAE77014; BAE77014

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
947423

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
ecj:JW2918
eco:b2951

Pathosystems Resource Integration Center (PATRIC)

More...
PATRICi
fig|1411691.4.peg.3781

<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
U28377 Genomic DNA Translation: AAA69118.1
U00096 Genomic DNA Translation: AAC75988.1
AP009048 Genomic DNA Translation: BAE77014.1
PIRiF65080
RefSeqiNP_417426.1, NC_000913.3
WP_000997795.1, NZ_STEB01000001.1

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
1W8GX-ray2.00A1-234[»]
3SY1X-ray1.46A1-234[»]
SMRiP67080
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

BioGridi4261786, 34 interactors
851744, 1 interactor
DIPiDIP-12194N
IntActiP67080, 9 interactors
STRINGi511145.b2951

Proteomic databases

jPOSTiP67080
PaxDbiP67080
PRIDEiP67080

Genome annotation databases

EnsemblBacteriaiAAC75988; AAC75988; b2951
BAE77014; BAE77014; BAE77014
GeneIDi947423
KEGGiecj:JW2918
eco:b2951
PATRICifig|1411691.4.peg.3781

Organism-specific databases

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

More...
EchoBASEi
EB2804

Phylogenomic databases

eggNOGiENOG4105DFA Bacteria
COG0325 LUCA
HOGENOMiHOG000048983
InParanoidiP67080
KOiK06997
PhylomeDBiP67080

Enzyme and pathway databases

BioCyciEcoCyc:G7527-MONOMER
ECOL316407:JW2918-MONOMER

Miscellaneous databases

EvolutionaryTraceiP67080

Protein Ontology

More...
PROi
PR:P67080

Family and domain databases

Gene3Di3.20.20.10, 1 hit
HAMAPiMF_02087 PLP_homeostasis, 1 hit
InterProiView protein in InterPro
IPR001608 Ala_racemase_N
IPR029066 PLP-binding_barrel
IPR011078 PyrdxlP_homeostasis
PANTHERiPTHR10146 PTHR10146, 1 hit
PfamiView protein in Pfam
PF01168 Ala_racemase_N, 1 hit
PIRSFiPIRSF004848 YBL036c_PLPDEIII, 1 hit
SUPFAMiSSF51419 SSF51419, 1 hit
TIGRFAMsiTIGR00044 TIGR00044, 1 hit
PROSITEiView protein in PROSITE
PS01211 UPF0001, 1 hit

ProtoNet; Automatic hierarchical classification of proteins

More...
ProtoNeti
Search...

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
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 nameiPLPHP_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: P67080
Secondary accession number(s): P52054, Q2M9P2
<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: October 11, 2004
Last sequence update: October 11, 2004
Last modified: November 13, 2019
This is version 114 of the entry and version 1 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. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries
  2. SIMILARITY comments
    Index of protein domains and families
  3. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  4. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
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