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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: Annotation score: 5 out of 5-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

Pathway: 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.

Pathway: 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)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei24 – 241Substrate1 Publication
Binding sitei29 – 291Substrate1 Publication
Binding sitei48 – 481Substrate1 Publication
Binding sitei50 – 501SubstrateBy similarity
Binding sitei60 – 601Substrate1 Publication
Binding sitei63 – 631SubstrateBy similarity
Sitei63 – 631Important in abstrating the protons in C3' and C5'
Binding sitei73 – 731SubstrateBy similarity
Binding sitei84 – 841SubstrateBy similarity
Binding sitei120 – 1201SubstrateBy similarity
Sitei133 – 1331May have a key role in proton donation to C5'

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
Complete GO annotation...

Keywords - Molecular functioni

Isomerase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Enzyme and pathway databases

BioCyciSENT99287:GCTI-2106-MONOMER.
SABIO-RKP26394.
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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014 Componenti: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi63 – 631H → A: Loss of epimerase activity. 1 Publication
Mutagenesisi73 – 731K → A: Reduces the epimerase activity by over 100-fold. 1 Publication
Mutagenesisi133 – 1331Y → F: Reduces the epimerase activity by over 1000-fold. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 183183dTDP-4-dehydrorhamnose 3,5-epimerasePRO_0000207979Add
BLAST

Proteomic databases

PaxDbiP26394.
PRIDEiP26394.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi99287.STM2094.

Structurei

Secondary structure

1
183
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi3 – 64Combined sources
Beta strandi13 – 164Combined sources
Beta strandi19 – 224Combined sources
Beta strandi25 – 328Combined sources
Helixi33 – 408Combined sources
Beta strandi48 – 558Combined sources
Beta strandi58 – 658Combined sources
Helixi67 – 693Combined sources
Beta strandi73 – 8816Combined sources
Turni94 – 974Combined sources
Beta strandi99 – 1057Combined sources
Turni106 – 1083Combined sources
Beta strandi111 – 1144Combined sources
Beta strandi118 – 1247Combined sources
Beta strandi126 – 13712Combined sources
Turni141 – 1433Combined sources
Beta strandi144 – 1463Combined sources
Turni152 – 1554Combined sources
Helixi168 – 1714Combined sources
Helixi176 – 1783Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP26394.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni169 – 1702Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1898.
HOGENOMiHOG000227724.
KOiK01790.
OMAiKVFPDER.
OrthoDBiEOG6HTP2V.
PhylomeDBiP26394.

Family and domain databases

Gene3Di2.60.120.10. 1 hit.
InterProiIPR000888. dTDP_sugar_isom.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PANTHERiPTHR21047. PTHR21047. 1 hit.
PfamiPF00908. dTDP_sugar_isom. 1 hit.
[Graphical view]
ProDomiPD001462. dTDP_sugar_isom. 1 hit.
[Graphical view] [Entries sharing at least one domain]
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_003197.1.
WP_000973708.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL20998; AAL20998; STM2094.
GeneIDi1253615.
KEGGistm:STM2094.
PATRICi32382771. VBISalEnt20916_2216.

Cross-referencesi

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_003197.1.
WP_000973708.1. NC_003197.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi99287.STM2094.

Proteomic databases

PaxDbiP26394.
PRIDEiP26394.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAL20998; AAL20998; STM2094.
GeneIDi1253615.
KEGGistm:STM2094.
PATRICi32382771. VBISalEnt20916_2216.

Phylogenomic databases

eggNOGiCOG1898.
HOGENOMiHOG000227724.
KOiK01790.
OMAiKVFPDER.
OrthoDBiEOG6HTP2V.
PhylomeDBiP26394.

Enzyme and pathway databases

UniPathwayiUPA00124.
UPA00281.
BioCyciSENT99287:GCTI-2106-MONOMER.
SABIO-RKP26394.

Miscellaneous databases

EvolutionaryTraceiP26394.

Family and domain databases

Gene3Di2.60.120.10. 1 hit.
InterProiIPR000888. dTDP_sugar_isom.
IPR014710. RmlC-like_jellyroll.
IPR011051. RmlC_Cupin.
[Graphical view]
PANTHERiPTHR21047. PTHR21047. 1 hit.
PfamiPF00908. dTDP_sugar_isom. 1 hit.
[Graphical view]
ProDomiPD001462. dTDP_sugar_isom. 1 hit.
[Graphical view] [Entries sharing at least one domain]
SUPFAMiSSF51182. SSF51182. 1 hit.
TIGRFAMsiTIGR01221. rmlC. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Structure and sequence of the rfb (O antigen) gene cluster of Salmonella serovar typhimurium (strain LT2)."
    Jiang X.-M., Neal B., Santiago F., Lee S.J., Romana L.K., Reeves P.R.
    Mol. Microbiol. 5:695-713(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: LT2.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: LT2 / SGSC1412 / ATCC 700720.
  3. "RmlC, a C3' and C5' carbohydrate epimerase, appears to operate via an intermediate with an unusual twist boat conformation."
    Dong C., Major L.L., Srikannathasan V., Errey J.C., Giraud M.F., Lam J.S., Graninger M., Messner P., McNeil M.R., Field R.A., Whitfield C., Naismith J.H.
    J. Mol. Biol. 365:146-159(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: MUTAGENESIS OF HIS-63; LYS-73 AND TYR-133, FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS, CATALYTIC ACTIVITY, REACTION MECHANISM.
  4. "RmlC, the third enzyme of dTDP-L-rhamnose pathway, is a new class of epimerase."
    Giraud M.-F., Leonard G.A., Field R.A., Berlind C., Naismith J.H.
    Nat. Struct. Biol. 7:398-402(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.17 ANGSTROMS) IN COMPLEX WITH SUBSTRATE, SUBUNIT.

Entry informationi

Entry nameiRMLC_SALTY
AccessioniPrimary (citable) accession number: P26394
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: May 27, 2015
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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 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.