Pseudomonas aeruginosa PAO1, PA4239 (rpsD)

Cytoplasmic
Cytoplasmic Membrane
Periplasmic
Outer Membrane
Extracellular
Unknown
View in JBrowse PseudoCyc / Metabolic Pathways

Gene Feature Overview

Strain Pseudomonas aeruginosa PAO1 (Stover et al., 2000)
GCF_000006765.1|latest
Locus Tag
PA4239
Name
rpsD
Replicon chromosome
Genomic location 4755447 - 4756067 (- strand)
Transposon Mutants in orthologs 1 transposon mutants in orthologs

Cross-References

RefSeq NP_252929.1
GI 15599435
Affymetrix PA4239_rpsD_at
DNASU PaCD00007838
Entrez 881814
GenBank AAG07627.1
INSDC AAC03115.1
NCBI Locus Tag PA4239
protein_id(GenBank) gb|AAG07627.1|AE004841_5|gnl|PseudoCAP|PA4239
TIGR NTL03PA04240
UniParc UPI0000135015
UniProtKB Acc O52759
UniProtKB ID RS4_PSEAE
UniRef100 UniRef100_B7V667
UniRef50 UniRef50_P44373
UniRef90 UniRef90_A6UZL2

Product

Feature Type CDS
Coding Frame 1
Product Name
30S ribosomal protein S4
Product Name Confidence: Class 2
Synonyms
Evidence for Translation
Detected using LC-MS/MS (23.28 kDa, PMID:21751344)
Identified using nanoflow high-pressure liquid chromatography (HPLC) in conjunction with microelectrospray ionization on LTQ XL mass spectrometer (PMID:24291602).
Charge (pH 7) 16.35
Kyte-Doolittle Hydrophobicity Value -0.677
Molecular Weight (kDa) 23.3
Isoelectric Point (pI) 10.48

Subcellular localization

Individual Mappings
Localization Confidence PMID
Cytoplasmic Class 3
Outer Membrane Vesicle Class 1
Additional evidence for subcellular localization

AlphaFold 2 Protein Structure Predictions

Protein structure predictions using a neural network model developed by DeepMind. If a UniProtKB accession is associated with this protein, a search link will be provided below.

Look for predicted 3D structure in AlphaFold DB: Search

PDB 3D Structures

Accession Header Accession Date Compound Source Resolution Method Percent Identity
6SPE RIBOSOME 09/01/19 Pseudomonas aeruginosa 30s ribosome from a clinical isolate Pseudomonas aeruginosa 3.6 ELECTRON MICROSCOPY 100.0
7UNU RIBOSOME 04/11/22 Pseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (composite structure I-B) Escherichia coli; Pseudomonas aeruginosa PAO1; SYNTHETIC CONSTRUCT 2.9 ELECTRON MICROSCOPY 100.0
6SPG RIBOSOME 09/01/19 Pseudomonas aeruginosa 70s ribosome from a clinical isolate Pseudomonas aeruginosa 3.34 ELECTRON MICROSCOPY 100.0
7UNR RIBOSOME 04/11/22 Pseudomonas aeruginosa 70S ribosome initiation complex bound to compact IF2-GDP (composite structure I-A) Escherichia coli; Pseudomonas aeruginosa PAO1; SYNTHETIC CONSTRUCT 2.9 ELECTRON MICROSCOPY 100.0
6SPF RIBOSOME 09/01/19 Pseudomonas aeruginosa 70s ribosome from an aminoglycoside resistant clinical isolate Pseudomonas aeruginosa 2.89 ELECTRON MICROSCOPY 100.0
7UNV RIBOSOME 04/11/22 Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-A) Escherichia coli; Pseudomonas aeruginosa PAO1; SYNTHETIC CONSTRUCT 2.7 ELECTRON MICROSCOPY 100.0
6SPC RIBOSOME 09/01/19 Pseudomonas aeruginosa 30s ribosome from an aminoglycoside resistant clinical isolate Pseudomonas aeruginosa 2.95 ELECTRON MICROSCOPY 100.0
7UNW RIBOSOME 04/11/22 Pseudomonas aeruginosa 70S ribosome initiation complex bound to IF2-GDPCP (structure II-B) Escherichia coli; Pseudomonas aeruginosa PAO1; SYNTHETIC CONSTRUCT 2.6 ELECTRON MICROSCOPY 100.0

Drugs Targeting this Protein

Identified by Diamond using e-value cutoff of 0.0001 and returning alignments that span 100% of the query sequence and that have more than 95% identity.

Drug Name Source Accession Source DB Version Target Accession Target Description Percent Identity Alignment Length E-Value
2-METHYLTHIO-N6-ISOPENTENYL-ADENOSINE-5'-MONOPHOSPHATE DB08185 DrugBank 5.1.4 P80373 30S ribosomal protein S4 52.9 210 6.3e-52

Pathogen Association Analysis

Results
Common
Found in both pathogen and nonpathogenic strains
Hits to this gene were found in 611 genera

Orthologs/Comparative Genomics

Pseudomonas Ortholog Database View orthologs at Pseudomonas Ortholog Database
Pseudomonas Ortholog Group POG001471 (536 members)
Putative Inparalogs None Found

Interactions

STRING database Search for predicted protein-protein interactions using:
Search term: PA4239
Search term: rpsD

Human Homologs

References

Regulation of alpha operon gene expression in Escherichia coli. A novel form of translational coupling.
Thomas MS, Bedwell DM, Nomura M
J Mol Biol 1987 Jul 20;196(2):333-45
PubMed ID: 3309351
Mutations in ribosomal proteins S4 and S12 influence the higher order structure of 16 S ribosomal RNA.
Allen PN, Noller HF
J Mol Biol 1989 Aug 5;208(3):457-68
PubMed ID: 2477554
Proteomic analysis of outer membrane vesicles derived from Pseudomonas aeruginosa.
Choi DS, Kim DK, Choi SJ, Lee J, Choi JP, Rho S, Park SH, Kim YK, Hwang D, Gho YS
Proteomics 2011 Aug;11(16):3424-9
PubMed ID: 21751344