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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-Experimental evidence at protein leveli

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

GO - Molecular functioni

  • pyridoxal phosphate binding Source: EcoCyc

Keywordsi

LigandPyridoxal phosphate

Enzyme and pathway databases

BioCyciEcoCyc:G7527-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Pyridoxal phosphate homeostasis proteinUniRule annotationCurated
Short name:
PLP homeostasis proteinUniRule annotationCurated
Gene namesi
Name:yggS
Ordered Locus Names:b2951, JW2918
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12979. yggS.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc

Pathology & Biotechi

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
Mutagenesisi36K → A: Does not bind PLP. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001631961 – 234Pyridoxal phosphate homeostasis proteinAdd BLAST234

Amino acid modifications

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Modified residuei36N6-(pyridoxal phosphate)lysineUniRule annotationCombined sources1 Publication1

Proteomic databases

PaxDbiP67080.
PRIDEiP67080.

Interactioni

Subunit structurei

Monomer.UniRule annotation1 Publication

Protein-protein interaction databases

BioGridi4261786. 34 interactors.
DIPiDIP-12194N.
IntActiP67080. 9 interactors.
MINTiMINT-1236179.
STRINGi316385.ECDH10B_3126.

Structurei

Secondary structure

1234
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi3 – 21Combined sources19
Helixi26 – 28Combined sources3
Beta strandi30 – 34Combined sources5
Helixi40 – 48Combined sources9
Beta strandi53 – 58Combined sources6
Helixi59 – 72Combined sources14
Beta strandi78 – 81Combined sources4
Helixi87 – 89Combined sources3
Helixi90 – 96Combined sources7
Beta strandi98 – 103Combined sources6
Helixi106 – 115Combined sources10
Beta strandi123 – 129Combined sources7
Beta strandi138 – 140Combined sources3
Helixi142 – 144Combined sources3
Helixi145 – 153Combined sources9
Beta strandi158 – 164Combined sources7
Helixi173 – 191Combined sources19
Beta strandi199 – 201Combined sources3
Helixi205 – 207Combined sources3
Helixi208 – 214Combined sources7
Beta strandi218 – 222Combined sources5
Helixi223 – 226Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1W8GX-ray2.00A1-234[»]
3SY1X-ray1.46A1-234[»]
ProteinModelPortaliP67080.
SMRiP67080.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP67080.

Family & Domainsi

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DFA. Bacteria.
COG0325. LUCA.
HOGENOMiHOG000048983.
InParanoidiP67080.
KOiK06997.
PhylomeDBiP67080.

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.

Sequencei

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
Checksum:i2AA431E2D75BCA59
GO

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_LN832404.1.

Genome annotation databases

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

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.

Entry informationi

Entry nameiPLPHP_ECOLI
AccessioniPrimary (citable) accession number: P67080
Secondary accession number(s): P52054, Q2M9P2
Entry historyiIntegrated into UniProtKB/Swiss-Prot: October 11, 2004
Last sequence update: October 11, 2004
Last modified: July 5, 2017
This is version 103 of the entry and version 1 of the sequence. See 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. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families
  4. Uncharacterized protein families (UPF)
    List of uncharacterized protein family (UPF) entries