Pseudomonas aeruginosa PAO1, PA5164 (rmlC)

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
PA5164
Name
rmlC
Synonym: rfbC
Replicon chromosome
Genomic location 5813122 - 5813667 (+ strand)
Transposon Mutants 1 transposon mutants in PAO1

Cross-References

RefSeq NP_253851.1
GI 15600357
Affymetrix PA5164_rmlC_at
DNASU PaCD00008220
Entrez 879991
GenBank AAG08549.1
INSDC AAG08549.1
NCBI Locus Tag PA5164
protein_id(GenBank) gb|AAG08549.1|AE004929_4|gnl|PseudoCAP|PA5164
TIGR NTL03PA05165
UniParc UPI00000DCE21
UniProtKB Acc Q9HU21
UniProtKB ID RMLC_PSEAE
UniRef100 UniRef100_Q9HU21
UniRef50 UniRef50_Q9HU21
UniRef90 UniRef90_Q9HU21

Product

Feature Type CDS
Coding Frame 1
Product Name
dTDP-4-dehydrorhamnose 3,5-epimerase
Product Name Confidence: Class 1
Synonyms dTDP-4-keto-6-deoxyglucose 3,5-epimerase
dTDP-L-rhamnose synthetase
Evidence for Translation
Identified using nanoflow high-pressure liquid chromatography (HPLC) in conjunction with microelectrospray ionization on LTQ XL mass spectrometer (PMID:24291602).
Charge (pH 7) -2.89
Kyte-Doolittle Hydrophobicity Value -0.383
Molecular Weight (kDa) 20.8
Isoelectric Point (pI) 6.02

Subcellular localization

Individual Mappings
Localization Confidence PMID
Unknown Class 3
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
1RTV ISOMERASE 12/10/03 RmlC (dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase) crystal structure from Pseudomonas aeruginosa, apo structure Pseudomonas aeruginosa 2.5 X-RAY DIFFRACTION 100.0
2IXI ISOMERASE 07/08/06 RmlC P aeruginosa with dTDP-xylose PSEUDOMONAS AERUGINOSA 1.8 X-RAY DIFFRACTION 100.0
6DIN ISOMERASE 05/23/18 High resolutionstructure of apo dTDP-4-dehydrorhamnose 3,5-epimerase Pseudomonas aeruginosa 1.8 X-RAY DIFFRACTION 100.0
2IXH ISOMERASE 07/08/06 RmlC P aeruginosa with dTDP-rhamnose PSEUDOMONAS AERUGINOSA 2 X-RAY DIFFRACTION 100.0
2IXK ISOMERASE 07/08/06 RmlC P aeruginosa with dTDP-4-keto rhamnnose (the product of the reaction) PSEUDOMONAS AERUGINOSA 1.7 X-RAY DIFFRACTION 100.0
2IXJ ISOMERASE 07/08/06 RmlC P aeruginosa native PSEUDOMONAS AERUGINOSA 2.54 X-RAY DIFFRACTION 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
D-tartaric acid DB01694 DrugBank 5.1.4 Q9HU21 dTDP-4-dehydrorhamnose 3,5-epimerase 100.0 181 3.2e-105

Pathogen Association Analysis

Results
Common
Found in both pathogen and nonpathogenic strains
Hits to this gene were found in 473 genera

Orthologs/Comparative Genomics

Pseudomonas Ortholog Database View orthologs at Pseudomonas Ortholog Database
Pseudomonas Ortholog Group POG004755 (533 members)
Putative Inparalogs None Found

Interactions

STRING database Search for predicted protein-protein interactions using:
Search term: PA5164
Search term: rmlC

Human Homologs

References

Involvement of the rml locus in core oligosaccharide and O polysaccharide assembly in Pseudomonas aeruginosa.
Rahim R, Burrows LL, Monteiro MA, Perry MB, Lam JS
Microbiology (Reading) 2000 Nov;146 ( Pt 11):2803-2814
PubMed ID: 11065359
Nucleotide sequence of the rhamnose biosynthetic operon of Shigella flexneri 2a and role of lipopolysaccharide in virulence.
Rajakumar K, Jost BH, Sasakawa C, Okada N, Yoshikawa M, Adler B
J Bacteriol 1994 Apr;176(8):2362-73
PubMed ID: 8157605
Genetic analysis of the O-specific lipopolysaccharide biosynthesis region (rfb) of Escherichia coli K-12 W3110: identification of genes that confer group 6 specificity to Shigella flexneri serotypes Y and 4a.
Yao Z, Valvano MA
J Bacteriol 1994 Jul;176(13):4133-43
PubMed ID: 7517390
RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation.
Dong C, Major LL, Srikannathasan V, Errey JC, Giraud MF, Lam JS, Graninger M, Messner P, McNeil MR, Field RA, Whitfield C, Naismith JH
J Mol Biol 2007 Jan 5;365(1):146-59
PubMed ID: 17046787