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Protein

dTDP-4-dehydrorhamnose 3,5-epimerase

Gene

rfbC

Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the epimerization of the C3' and C5'positions of dTDP-6-deoxy-D-xylo-4-hexulose, forming dTDP-6-deoxy-L-lyxo-4-hexulose.1 Publication

Catalytic activityi

dTDP-4-dehydro-6-deoxy-alpha-D-glucose = dTDP-4-dehydro-beta-L-rhamnose.1 Publication

Pathwayi: dTDP-L-rhamnose biosynthesis

This protein is involved in the pathway dTDP-L-rhamnose biosynthesis, which is part of Carbohydrate biosynthesis.
View all proteins of this organism that are known to be involved in the pathway dTDP-L-rhamnose biosynthesis and in Carbohydrate biosynthesis.

Pathwayi: LPS O-antigen biosynthesis

This protein is involved in the pathway LPS O-antigen biosynthesis, which is part of Bacterial outer membrane biogenesis.
View all proteins of this organism that are known to be involved in the pathway LPS O-antigen biosynthesis and in Bacterial outer membrane biogenesis.

Sites

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Binding sitei24Substrate1 Publication1
Binding sitei29Substrate1 Publication1
Binding sitei48Substrate1 Publication1
Binding sitei50SubstrateBy similarity1
Binding sitei60Substrate1 Publication1
Binding sitei63SubstrateBy similarity1
Sitei63Important in abstrating the protons in C3' and C5'1
Binding sitei73SubstrateBy similarity1
Binding sitei84SubstrateBy similarity1
Binding sitei120SubstrateBy similarity1
Sitei133May have a key role in proton donation to C5'1

GO - Molecular functioni

  • dTDP-4-dehydrorhamnose 3,5-epimerase activity Source: UniProtKB

GO - Biological processi

  • dTDP-rhamnose biosynthetic process Source: UniProtKB-UniPathway
  • extracellular polysaccharide biosynthetic process Source: UniProtKB
  • lipopolysaccharide biosynthetic process Source: UniProtKB
  • O antigen biosynthetic process Source: UniProtKB-UniPathway

Keywordsi

Molecular functionIsomerase
Biological processLipopolysaccharide biosynthesis

Enzyme and pathway databases

BioCyciSENT99287:G1FZD-2113-MONOMER
SABIO-RKiP26394
UniPathwayiUPA00124
UPA00281

Names & Taxonomyi

Protein namesi
Recommended name:
dTDP-4-dehydrorhamnose 3,5-epimerase (EC:5.1.3.13)
Alternative name(s):
Thymidine diphospho-4-keto-rhamnose 3,5-epimerase
dTDP-4-keto-6-deoxyglucose 3,5-epimerase
dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase
dTDP-L-rhamnose synthase
Gene namesi
Name:rfbC
Synonyms:rmlC
Ordered Locus Names:STM2094
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeSalmonella
Proteomesi
  • UP000001014 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi63H → A: Loss of epimerase activity. 1 Publication1
Mutagenesisi73K → A: Reduces the epimerase activity by over 100-fold. 1 Publication1
Mutagenesisi133Y → F: Reduces the epimerase activity by over 1000-fold. 1 Publication1

Chemistry databases

DrugBankiDB02549 3'-O-Acetylthymidine-5'-Diphosphate

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002079791 – 183dTDP-4-dehydrorhamnose 3,5-epimeraseAdd BLAST183

Proteomic databases

PaxDbiP26394
PRIDEiP26394

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi99287.STM2094

Structurei

Secondary structure

1183
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi3 – 6Combined sources4
Beta strandi13 – 16Combined sources4
Beta strandi19 – 22Combined sources4
Beta strandi25 – 32Combined sources8
Helixi33 – 40Combined sources8
Beta strandi48 – 55Combined sources8
Beta strandi58 – 65Combined sources8
Helixi67 – 69Combined sources3
Beta strandi73 – 88Combined sources16
Turni94 – 97Combined sources4
Beta strandi99 – 105Combined sources7
Turni106 – 108Combined sources3
Beta strandi111 – 114Combined sources4
Beta strandi118 – 124Combined sources7
Beta strandi126 – 137Combined sources12
Turni141 – 143Combined sources3
Beta strandi144 – 146Combined sources3
Turni152 – 155Combined sources4
Helixi168 – 171Combined sources4
Helixi176 – 178Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1DZRX-ray2.17A/B1-183[»]
1DZTX-ray2.20A/B1-183[»]
ProteinModelPortaliP26394
SMRiP26394
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiP26394

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni169 – 170Substrate binding2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4108URP Bacteria
COG1898 LUCA
HOGENOMiHOG000227724
KOiK01790
OMAiGDDRGYF
PhylomeDBiP26394

Family and domain databases

Gene3Di2.60.120.10, 1 hit
InterProiView protein in InterPro
IPR000888 dTDP_sugar_isom
IPR014710 RmlC-like_jellyroll
IPR011051 RmlC_Cupin_sf
PANTHERiPTHR21047 PTHR21047, 1 hit
PfamiView protein in Pfam
PF00908 dTDP_sugar_isom, 1 hit
ProDomiView protein in ProDom or Entries sharing at least one domain
PD001462 dTDP_sugar_isom, 1 hit
SUPFAMiSSF51182 SSF51182, 1 hit
TIGRFAMsiTIGR01221 rmlC, 1 hit

Sequencei

Sequence statusi: Complete.

P26394-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMIVIKTAIP DVLILEPKVF GDERGFFFES YNQQTFEELI GRKVTFVQDN
60 70 80 90 100
HSKSKKNVLR GLHFQRGENA QGKLVRCAVG EVFDVAVDIR KESPTFGQWV
110 120 130 140 150
GVNLSAENKR QLWIPEGFAH GFVTLSEYAE FLYKATNYYS PSSEGSILWN
160 170 180
DEAIGIEWPF SQLPELSAKD AAAPLLDQAL LTE
Length:183
Mass (Da):20,663
Last modified:August 1, 1992 - v1
Checksum:i0176B52C38038C77
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X56793 Genomic DNA Translation: CAA40118.1
AE006468 Genomic DNA Translation: AAL20998.1
PIRiS15302
RefSeqiNP_461039.1, NC_003197.2
WP_000973708.1, NC_003197.2

Genome annotation databases

EnsemblBacteriaiAAL20998; AAL20998; STM2094
GeneIDi1253615
KEGGistm:STM2094
PATRICifig|99287.12.peg.2216

Similar proteinsi

Entry informationi

Entry nameiRMLC_SALTY
AccessioniPrimary (citable) accession number: P26394
Entry historyiIntegrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: March 28, 2018
This is version 123 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
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Main funding by: National Institutes of Health