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Protein

dTDP-4-dehydrorhamnose reductase

Gene

rfbD

Organism
Shigella flexneri
Status
Reviewed-Annotation score: Annotation score: 4 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.

Cofactori

Mg2+By similarityNote: Binds 1 Mg2+ ion per monomer.By similarity

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 sitei12NAD; via amide nitrogenBy similarity1
Binding sitei102NADP; via carbonyl oxygenBy similarity1
Binding sitei153Substrate; via amide nitrogenBy similarity1
Binding sitei154NAD; via amide nitrogenBy similarity1
Binding sitei223SubstrateBy similarity1
Binding sitei260SubstrateBy similarity1

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Nucleotide bindingi7 – 13NADPSequence analysis7
Nucleotide bindingi7 – 11NADBy similarity5
Nucleotide bindingi11 – 12NADPBy similarity2
Nucleotide bindingi30 – 31NADBy similarity2
Nucleotide bindingi39 – 40NAD/NADPBy similarity2
Nucleotide bindingi62 – 65NADBy similarity4
Nucleotide bindingi63 – 65NADPBy similarity3
Nucleotide bindingi128 – 132NAD/NADPBy similarity5

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Lipopolysaccharide biosynthesis

Keywords - Ligandi

NADP

Enzyme and pathway databases

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
Ordered Locus Names:SF2103, S2226
OrganismiShigella flexneri
Taxonomic identifieri623 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeShigella
Proteomesi
  • UP000002673 Componenti: Chromosome
  • UP000001006 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002079871 – 299dTDP-4-dehydrorhamnose reductaseAdd BLAST299

Proteomic databases

PaxDbiP37778.
PRIDEiP37778.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi198214.SF2103.

Structurei

3D structure databases

ProteinModelPortaliP37778.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni104 – 105Substrate bindingBy similarity2

Sequence similaritiesi

Phylogenomic databases

eggNOGiENOG4105DBZ. Bacteria.
COG1091. LUCA.
HOGENOMiHOG000227712.
KOiK00067.
OMAiGYASRYE.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR005913. dTDP_dehydrorham_reduct.
IPR016040. NAD(P)-bd_dom.
IPR029903. RmlD-like-bd.
[Graphical view]
PANTHERiPTHR10491. PTHR10491. 1 hit.
PfamiPF04321. RmlD_sub_bind. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01214. rmlD. 1 hit.

Sequencei

Sequence statusi: Complete.

P37778-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MNILLFGKTG QVGWELQRAL APLGNLIALD VHSTDYCGDF SNPEGVAETV
60 70 80 90 100
KKIRPDVIVN AAAHTAVDKA ESEPNFAQLL NATCVEAIAK AANEVGAWVI
110 120 130 140 150
HYSTDYVFPG NGDTPWLETD ATAPLNVYGE TKLAGEKALQ EHCAKHLIFR
160 170 180 190 200
TSWVYAGKGN NFAKTMLRLA KEREELAVIN DQFGAPTGAE LLADCTAHAI
210 220 230 240 250
RVAANKPEVA GLYHLVAGGT TTWHDYAALV FEEARRAGIN LALNKLNAVP
260 270 280 290
TTAYPTPARR PHNSRLNTEK FQQNFALVLP DWQVGVKRML NELFTTTAI
Length:299
Mass (Da):32,565
Last modified:January 10, 2003 - v2
Checksum:iF2C6EF7BA8BD54DE
GO

Experimental Info

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Sequence conflicti89A → I in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti115P → A in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti130E → G in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti135 – 136GE → WG in CAA50768 (PubMed:8170390).Curated2
Sequence conflicti141E → D in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti144A → G in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti172E → D in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti175E → T in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti180N → T in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti190E → LD in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti197A → R in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti201 – 202RV → WL in CAA50768 (PubMed:8170390).Curated2
Sequence conflicti227A → P in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti232E → K in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti239I → F in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti242A → P in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti260R → G in CAA50768 (PubMed:8170390).Curated1
Sequence conflicti264S → F in CAA50768 (PubMed:8170390).Curated1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71970 Genomic DNA. Translation: CAA50768.1.
L14842 Genomic DNA. Translation: AAA53680.1.
AE005674 Genomic DNA. Translation: AAN43642.1.
AE014073 Genomic DNA. Translation: AAP17471.1.
PIRiC55213.
S41535.
RefSeqiNP_707935.1. NC_004337.2.
WP_001023623.1. NZ_LVJC01000030.1.

Genome annotation databases

EnsemblBacteriaiAAN43642; AAN43642; SF2103.
AAP17471; AAP17471; S2226.
GeneIDi1025316.
KEGGisfl:SF2103.
sft:NCTC1_02311.
sfx:S2226.
PATRICi18705959. VBIShiFle31049_2458.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X71970 Genomic DNA. Translation: CAA50768.1.
L14842 Genomic DNA. Translation: AAA53680.1.
AE005674 Genomic DNA. Translation: AAN43642.1.
AE014073 Genomic DNA. Translation: AAP17471.1.
PIRiC55213.
S41535.
RefSeqiNP_707935.1. NC_004337.2.
WP_001023623.1. NZ_LVJC01000030.1.

3D structure databases

ProteinModelPortaliP37778.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198214.SF2103.

Proteomic databases

PaxDbiP37778.
PRIDEiP37778.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAN43642; AAN43642; SF2103.
AAP17471; AAP17471; S2226.
GeneIDi1025316.
KEGGisfl:SF2103.
sft:NCTC1_02311.
sfx:S2226.
PATRICi18705959. VBIShiFle31049_2458.

Phylogenomic databases

eggNOGiENOG4105DBZ. Bacteria.
COG1091. LUCA.
HOGENOMiHOG000227712.
KOiK00067.
OMAiGYASRYE.

Enzyme and pathway databases

UniPathwayiUPA00124.
UPA00281.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR005913. dTDP_dehydrorham_reduct.
IPR016040. NAD(P)-bd_dom.
IPR029903. RmlD-like-bd.
[Graphical view]
PANTHERiPTHR10491. PTHR10491. 1 hit.
PfamiPF04321. RmlD_sub_bind. 1 hit.
[Graphical view]
SUPFAMiSSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01214. rmlD. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiRMLD_SHIFL
AccessioniPrimary (citable) accession number: P37778
Secondary accession number(s): Q54163
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 1, 1994
Last sequence update: January 10, 2003
Last modified: November 2, 2016
This is version 117 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. SIMILARITY comments
    Index of protein domains and families

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 one 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.