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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

Pathway:idTDP-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:iLPS 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 sitei12 – 121NAD; via amide nitrogenBy similarity
Binding sitei102 – 1021NADP; via carbonyl oxygenBy similarity
Binding sitei153 – 1531Substrate; via amide nitrogenBy similarity
Binding sitei154 – 1541NAD; via amide nitrogenBy similarity
Binding sitei223 – 2231SubstrateBy similarity
Binding sitei260 – 2601SubstrateBy similarity

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi7 – 137NADPSequence Analysis
Nucleotide bindingi7 – 115NADBy similarity
Nucleotide bindingi11 – 122NADPBy similarity
Nucleotide bindingi30 – 312NADBy similarity
Nucleotide bindingi39 – 402NAD/NADPBy similarity
Nucleotide bindingi62 – 654NADBy similarity
Nucleotide bindingi63 – 653NADPBy similarity
Nucleotide bindingi128 – 1325NAD/NADPBy similarity

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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeShigella
ProteomesiUP000002673 Componenti: Chromosome UP000001006 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 299299dTDP-4-dehydrorhamnose reductasePRO_0000207987Add
BLAST

Proteomic databases

PaxDbiP37778.

Interactioni

Subunit structurei

Homodimer.By similarity

Protein-protein interaction databases

STRINGi198214.SF2103.

Structurei

3D structure databases

ProteinModelPortaliP37778.
SMRiP37778. Positions 1-297.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

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

Sequence similaritiesi

Phylogenomic databases

eggNOGiCOG1091.
HOGENOMiHOG000227712.
KOiK00067.
OMAiPYWRDSL.
OrthoDBiEOG6HTP2V.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
InterProiIPR005913. dTDP_dehydrorham_reduct.
IPR016040. NAD(P)-bd_dom.
IPR029900. RmlD.
IPR029903. RmlD-like-bd.
[Graphical view]
PANTHERiPTHR10491. PTHR10491. 1 hit.
PTHR10491:SF5. PTHR10491:SF5. 1 hit.
PfamiPF04321. RmlD_sub_bind. 1 hit.
[Graphical view]
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)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti89 – 891A → I in CAA50768 (PubMed:8170390).Curated
Sequence conflicti115 – 1151P → A in CAA50768 (PubMed:8170390).Curated
Sequence conflicti130 – 1301E → G in CAA50768 (PubMed:8170390).Curated
Sequence conflicti135 – 1362GE → WG in CAA50768 (PubMed:8170390).Curated
Sequence conflicti141 – 1411E → D in CAA50768 (PubMed:8170390).Curated
Sequence conflicti144 – 1441A → G in CAA50768 (PubMed:8170390).Curated
Sequence conflicti172 – 1721E → D in CAA50768 (PubMed:8170390).Curated
Sequence conflicti175 – 1751E → T in CAA50768 (PubMed:8170390).Curated
Sequence conflicti180 – 1801N → T in CAA50768 (PubMed:8170390).Curated
Sequence conflicti190 – 1901E → LD in CAA50768 (PubMed:8170390).Curated
Sequence conflicti197 – 1971A → R in CAA50768 (PubMed:8170390).Curated
Sequence conflicti201 – 2022RV → WL in CAA50768 (PubMed:8170390).Curated
Sequence conflicti227 – 2271A → P in CAA50768 (PubMed:8170390).Curated
Sequence conflicti232 – 2321E → K in CAA50768 (PubMed:8170390).Curated
Sequence conflicti239 – 2391I → F in CAA50768 (PubMed:8170390).Curated
Sequence conflicti242 – 2421A → P in CAA50768 (PubMed:8170390).Curated
Sequence conflicti260 – 2601R → G in CAA50768 (PubMed:8170390).Curated
Sequence conflicti264 – 2641S → F in CAA50768 (PubMed:8170390).Curated

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_LM651928.1.

Genome annotation databases

EnsemblBacteriaiAAN43642; AAN43642; SF2103.
AAP17471; AAP17471; S2226.
GeneIDi1025316.
KEGGisfl:SF2103.
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_LM651928.1.

3D structure databases

ProteinModelPortaliP37778.
SMRiP37778. Positions 1-297.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi198214.SF2103.

Proteomic databases

PaxDbiP37778.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG1091.
HOGENOMiHOG000227712.
KOiK00067.
OMAiPYWRDSL.
OrthoDBiEOG6HTP2V.

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.
IPR029900. RmlD.
IPR029903. RmlD-like-bd.
[Graphical view]
PANTHERiPTHR10491. PTHR10491. 1 hit.
PTHR10491:SF5. PTHR10491:SF5. 1 hit.
PfamiPF04321. RmlD_sub_bind. 1 hit.
[Graphical view]
TIGRFAMsiTIGR01214. rmlD. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the dTDP-rhamnose biosynthetic genes encoded in the rfb locus of Shigella flexneri."
    Macpherson D.F., Manning P.A., Morona R.
    Mol. Microbiol. 11:281-292(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION IN DTDP-RHAMNOSE BIOSYNTHESIS.
    Strain: PE577 / Serotype 2a.
  2. "Nucleotide sequence of the rhamnose biosynthetic operon of Shigella flexneri 2a and role of lipopolysaccharide in virulence."
    Rajakumar K., Jost B.H., Sasakawa C., Okada N., Yoshikawa M., Adler B.
    J. Bacteriol. 176:2362-2373(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: YSH6200 / Serotype 2a.
  3. "Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157."
    Jin Q., Yuan Z., Xu J., Wang Y., Shen Y., Lu W., Wang J., Liu H., Yang J., Yang F., Zhang X., Zhang J., Yang G., Wu H., Qu D., Dong J., Sun L., Xue Y.
    , Zhao A., Gao Y., Zhu J., Kan B., Ding K., Chen S., Cheng H., Yao Z., He B., Chen R., Ma D., Qiang B., Wen Y., Hou Y., Yu J.
    Nucleic Acids Res. 30:4432-4441(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 301 / Serotype 2a.
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 700930 / 2457T / Serotype 2a.

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: July 22, 2015
This is version 109 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

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.