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P26392 (RMLD_SALTY) Reviewed, UniProtKB/Swiss-Prot

Last modified July 9, 2014. Version 106. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
dTDP-4-dehydrorhamnose reductase

EC=1.1.1.133
Alternative name(s):
dTDP-4-keto-L-rhamnose reductase
dTDP-6-deoxy-L-lyxo-4-hexulose reductase
dTDP-6-deoxy-L-mannose dehydrogenase
dTDP-L-rhamnose synthase
Gene names
Name:rfbD
Synonyms:rmlD
Ordered Locus Names:STM2096
OrganismSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720) [Reference proteome] [HAMAP]
Taxonomic identifier99287 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella

Protein attributes

Sequence length299 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well. Ref.3

Catalytic activity

dTDP-beta-L-rhamnose + NADP+ = dTDP-4-dehydro-beta-L-rhamnose + NADPH. Ref.3

Cofactor

Binds 1 magnesium ion per monomer. Ref.3

Pathway

Carbohydrate biosynthesis; dTDP-L-rhamnose biosynthesis.

Bacterial outer membrane biogenesis; LPS O-antigen biosynthesis.

Subunit structure

Homodimer. Ref.3

Sequence similarities

Belongs to the dTDP-4-dehydrorhamnose reductase family.

Biophysicochemical properties

Kinetic parameters:

KM=0.11 mM for dTDP-6-deoxy-L-mannose (at pH 6.5) Ref.3

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 299299dTDP-4-dehydrorhamnose reductase
PRO_0000207986

Regions

Nucleotide binding7 – 115NAD
Nucleotide binding11 – 122NADP
Nucleotide binding30 – 312NAD
Nucleotide binding39 – 402NAD/NADP
Nucleotide binding62 – 654NAD
Nucleotide binding63 – 653NADP
Nucleotide binding128 – 1325NAD/NADP
Region104 – 1052Substrate binding

Sites

Binding site121NAD; via amide nitrogen
Binding site1021NADP; via carbonyl oxygen
Binding site1531Substrate; via amide nitrogen
Binding site1541NAD; via amide nitrogen
Binding site2231Substrate
Binding site2601Substrate

Experimental info

Mutagenesis671V → A: Significantly reduces enzyme activity. Ref.3
Mutagenesis681D → A: Slightly reduces enzyme activity. Ref.3
Mutagenesis1041T → A: Loss of activity. Ref.3
Mutagenesis1281Y → F: Loss of activity. Ref.3
Mutagenesis1531W → A: Loss of activity. Ref.3

Secondary structure

....................................................... 299
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P26392 [UniParc].

Last modified August 1, 1992. Version 1.
Checksum: ABAA0476AF5ECDE7

FASTA29932,554
        10         20         30         40         50         60 
MNILLFGKTG QVGWELQRSL APVGNLIALD VHSKEFCGDF SNPKGVAETV RKLRPDVIVN 

        70         80         90        100        110        120 
AAAHTAVDKA ESEPELAQLL NATSVEAIAK AANETGAWVV HYSTDYVFPG TGDIPWQETD 

       130        140        150        160        170        180 
ATSPLNVYGK TKLAGEKALQ DNCPKHLIFR TSWVYAGKGN NFAKTMLRLA KERQTLSVIN 

       190        200        210        220        230        240 
DQYGAPTGAE LLADCTAHAI RVALNKPEVA GLYHLVAGGT TTWHDYAALV FDEARKAGIT 

       250        260        270        280        290 
LALTELNAVP TSAYPTPASR PGNSRLNTEK FQRNFDLILP QWELGVKRML TEMFTTTTI 

« Hide

References

« Hide 'large scale' references
[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]"Complete genome sequence of Salmonella enterica serovar Typhimurium LT2."
McClelland M., Sanderson K.E., Spieth J., Clifton S.W., Latreille P., Courtney L., Porwollik S., Ali J., Dante M., Du F., Hou S., Layman D., Leonard S., Nguyen C., Scott K., Holmes A., Grewal N., Mulvaney E. expand/collapse author list , Ryan E., Sun H., Florea L., Miller W., Stoneking T., Nhan M., Waterston R., Wilson R.K.
Nature 413:852-856(2001) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: LT2 / SGSC1412 / ATCC 700720.
[3]"Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode."
Blankenfeldt W., Kerr I.D., Giraud M.F., McMiken H.J., Leonard G., Whitfield C., Messner P., Graninger M., Naismith J.H.
Structure 10:773-786(2002) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) IN COMPLEXES WITH NADH, NADPH AND DTDP-L-RHAMNOSE, FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF VAL-67; ASP-68; THR-104; TYR-128 AND TRP-153, SUBUNIT, COFACTOR, REACTION MECHANISM.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
X56793 Genomic DNA. Translation: CAA40116.1.
AE006468 Genomic DNA. Translation: AAL21000.1.
PIRS15300.
RefSeqNP_461041.1. NC_003197.1.

3D structure databases

PDBe
RCSB-PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1KBZX-ray2.20A1-299[»]
1KC1X-ray2.60A1-299[»]
1KC3X-ray2.70A1-299[»]
1N2SX-ray2.00A1-299[»]
ProteinModelPortalP26392.
SMRP26392. Positions 1-298.
ModBaseSearch...
MobiDBSearch...

Protein-protein interaction databases

STRING99287.STM2096.

Proteomic databases

PaxDbP26392.
PRIDEP26392.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAL21000; AAL21000; STM2096.
GeneID1253617.
KEGGstm:STM2096.
PATRIC32382775. VBISalEnt20916_2218.

Phylogenomic databases

eggNOGCOG1091.
HOGENOMHOG000227712.
KOK00067.
OMAETTWHGY.
OrthoDBEOG6HTP2V.
PhylomeDBP26392.

Enzyme and pathway databases

BioCycRETL1328306-WGS:GSTH-1528-MONOMER.
SENT99287:GCTI-2108-MONOMER.
SABIO-RKP26392.
UniPathwayUPA00124.
UPA00281.

Family and domain databases

Gene3D3.40.50.720. 1 hit.
InterProIPR005913. dTDP_dehydrorham_reduct.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamPF04321. RmlD_sub_bind. 1 hit.
[Graphical view]
TIGRFAMsTIGR01214. rmlD. 1 hit.
ProtoNetSearch...

Other

EvolutionaryTraceP26392.

Entry information

Entry nameRMLD_SALTY
AccessionPrimary (citable) accession number: P26392
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: July 9, 2014
This is version 106 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

PATHWAY comments

Index of metabolic and biosynthesis pathways