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P26392

- RMLD_SALTY

UniProt

P26392 - RMLD_SALTY

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Protein

dTDP-4-dehydrorhamnose reductase

Gene
rfbD, rmlD, STM2096
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalyzes the reduction of dTDP-6-deoxy-L-lyxo-4-hexulose to yield dTDP-L-rhamnose. RmlD uses NADH and NADPH nearly equally well.1 Publication

Catalytic activityi

dTDP-beta-L-rhamnose + NADP+ = dTDP-4-dehydro-beta-L-rhamnose + NADPH.1 Publication

Cofactori

Binds 1 magnesium ion per monomer.1 Publication

Kineticsi

  1. KM=0.11 mM for dTDP-6-deoxy-L-mannose (at pH 6.5)1 Publication

Pathwayi

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei12 – 121NAD; via amide nitrogen
Binding sitei102 – 1021NADP; via carbonyl oxygen
Binding sitei153 – 1531Substrate; via amide nitrogen
Binding sitei154 – 1541NAD; via amide nitrogen
Binding sitei223 – 2231Substrate
Binding sitei260 – 2601Substrate

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi7 – 115NAD
Nucleotide bindingi11 – 122NADP
Nucleotide bindingi30 – 312NAD
Nucleotide bindingi39 – 402NAD/NADP
Nucleotide bindingi62 – 654NAD
Nucleotide bindingi63 – 653NADP
Nucleotide bindingi128 – 1325NAD/NADP

GO - Molecular functioni

  1. dTDP-4-dehydrorhamnose reductase activity Source: UniProtKB
  2. metal ion binding Source: UniProtKB-KW

GO - Biological processi

  1. dTDP-rhamnose biosynthetic process Source: UniProtKB-UniPathway
  2. extracellular polysaccharide biosynthetic process Source: UniProtKB
  3. lipopolysaccharide biosynthetic process Source: UniProtKB
  4. O antigen biosynthetic process Source: UniProtKB-UniPathway
Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Keywords - Ligandi

Magnesium, Metal-binding, NADP

Enzyme and pathway databases

BioCyciRETL1328306-WGS:GSTH-1528-MONOMER.
SENT99287:GCTI-2108-MONOMER.
SABIO-RKP26392.
UniPathwayiUPA00124.
UPA00281.

Names & Taxonomyi

Protein namesi
Recommended 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 namesi
Name:rfbD
Synonyms:rmlD
Ordered Locus Names:STM2096
OrganismiSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Taxonomic identifieri99287 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeSalmonella
ProteomesiUP000001014: Chromosome

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi67 – 671V → A: Significantly reduces enzyme activity. 1 Publication
Mutagenesisi68 – 681D → A: Slightly reduces enzyme activity. 1 Publication
Mutagenesisi104 – 1041T → A: Loss of activity. 1 Publication
Mutagenesisi128 – 1281Y → F: Loss of activity. 1 Publication
Mutagenesisi153 – 1531W → A: Loss of activity. 1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 299299dTDP-4-dehydrorhamnose reductasePRO_0000207986Add
BLAST

Proteomic databases

PaxDbiP26392.
PRIDEiP26392.

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi99287.STM2096.

Structurei

Secondary structure

1
299
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65
Helixi11 – 199
Turni20 – 234
Beta strandi24 – 296
Beta strandi34 – 363
Helixi43 – 5311
Beta strandi56 – 605
Helixi67 – 704
Helixi74 – 818
Helixi83 – 9210
Turni93 – 964
Beta strandi98 – 1047
Helixi105 – 1073
Beta strandi112 – 1143
Helixi127 – 14216
Beta strandi144 – 1518
Beta strandi153 – 1553
Beta strandi157 – 1593
Helixi162 – 17211
Beta strandi174 – 1796
Helixi189 – 20517
Helixi207 – 2093
Beta strandi211 – 2144
Helixi223 – 23715
Beta strandi245 – 2495
Helixi251 – 2533
Beta strandi262 – 2643
Helixi269 – 2757
Helixi282 – 29413

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1KBZX-ray2.20A1-299[»]
1KC1X-ray2.60A1-299[»]
1KC3X-ray2.70A1-299[»]
1N2SX-ray2.00A1-299[»]
ProteinModelPortaliP26392.
SMRiP26392. Positions 1-298.

Miscellaneous databases

EvolutionaryTraceiP26392.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni104 – 1052Substrate binding

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1091.
HOGENOMiHOG000227712.
KOiK00067.
OMAiETTWHGY.
OrthoDBiEOG6HTP2V.
PhylomeDBiP26392.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR005913. dTDP_dehydrorham_reduct.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF04321. RmlD_sub_bind. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01214. rmlD. 1 hit.

Sequencei

Sequence statusi: Complete.

P26392-1 [UniParc]FASTAAdd to Basket

« Hide

MNILLFGKTG QVGWELQRSL APVGNLIALD VHSKEFCGDF SNPKGVAETV    50
RKLRPDVIVN AAAHTAVDKA ESEPELAQLL NATSVEAIAK AANETGAWVV 100
HYSTDYVFPG TGDIPWQETD ATSPLNVYGK TKLAGEKALQ DNCPKHLIFR 150
TSWVYAGKGN NFAKTMLRLA KERQTLSVIN DQYGAPTGAE LLADCTAHAI 200
RVALNKPEVA GLYHLVAGGT TTWHDYAALV FDEARKAGIT LALTELNAVP 250
TSAYPTPASR PGNSRLNTEK FQRNFDLILP QWELGVKRML TEMFTTTTI 299
Length:299
Mass (Da):32,554
Last modified:August 1, 1992 - v1
Checksum:iABAA0476AF5ECDE7
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X56793 Genomic DNA. Translation: CAA40116.1.
AE006468 Genomic DNA. Translation: AAL21000.1.
PIRiS15300.
RefSeqiNP_461041.1. NC_003197.1.
WP_001023662.1. NC_003197.1.

Genome annotation databases

EnsemblBacteriaiAAL21000; AAL21000; STM2096.
GeneIDi1253617.
KEGGistm:STM2096.
PATRICi32382775. VBISalEnt20916_2218.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X56793 Genomic DNA. Translation: CAA40116.1 .
AE006468 Genomic DNA. Translation: AAL21000.1 .
PIRi S15300.
RefSeqi NP_461041.1. NC_003197.1.
WP_001023662.1. NC_003197.1.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1KBZ X-ray 2.20 A 1-299 [» ]
1KC1 X-ray 2.60 A 1-299 [» ]
1KC3 X-ray 2.70 A 1-299 [» ]
1N2S X-ray 2.00 A 1-299 [» ]
ProteinModelPortali P26392.
SMRi P26392. Positions 1-298.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

STRINGi 99287.STM2096.

Proteomic databases

PaxDbi P26392.
PRIDEi P26392.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AAL21000 ; AAL21000 ; STM2096 .
GeneIDi 1253617.
KEGGi stm:STM2096.
PATRICi 32382775. VBISalEnt20916_2218.

Phylogenomic databases

eggNOGi COG1091.
HOGENOMi HOG000227712.
KOi K00067.
OMAi ETTWHGY.
OrthoDBi EOG6HTP2V.
PhylomeDBi P26392.

Enzyme and pathway databases

UniPathwayi UPA00124 .
UPA00281 .
BioCyci RETL1328306-WGS:GSTH-1528-MONOMER.
SENT99287:GCTI-2108-MONOMER.
SABIO-RK P26392.

Miscellaneous databases

EvolutionaryTracei P26392.

Family and domain databases

Gene3Di 3.40.50.720. 1 hit.
InterProi IPR005913. dTDP_dehydrorham_reduct.
IPR016040. NAD(P)-bd_dom.
[Graphical view ]
Pfami PF04321. RmlD_sub_bind. 1 hit.
[Graphical view ]
TIGRFAMsi TIGR01214. rmlD. 1 hit.
ProtoNeti Search...

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. "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.

Entry informationi

Entry nameiRMLD_SALTY
AccessioniPrimary (citable) accession number: P26392
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: August 1, 1992
Last modified: September 3, 2014
This is version 107 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

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