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Escherichia coli K-12 substr. MG1655 Enzyme: dTDP-4-dehydrorhamnose reductase



Gene: rfbD Accession Numbers: EG12411 (EcoCyc), b2040, ECK2034

Synonyms: rmlD

Regulation Summary Diagram: ?

Component of: dTDP-L-rhamnose synthetase

Summary:
dTDP-4-dehydrorhamnose reductase (RfbD) is involved in the dTDP-rhamnose biosynthesis pathway, which is important for the synthesis of O-specific LPS. dTDP-4-dehydrorhamnose 3,5-epimerase forms a complex with dTDP-4-dehydrorhamnose reductase. The epimerase catalyzes inversion at C-3 and C-5 via corresponding enediols. The reductase then catalyzes the stereospecific reduction of the 4-keto group of epimerase-bound dTDP-4-dehydro-6-deoxy-L-mannose to generate the final product, dTDP-L-rhamnose. [Webb92, Glaser72, Giraud00, Stern99]

The genes encoding the enzymes involved in the biosynthesis of O-specific polysaccharides are clustered in the rfb region. E. coli K-12 does not normally express O-specific LPS due to mutations in the rfb region. However, genes responsible for the dTDP-rhamnose biosynthesis pathway have been identified [Stevenson94].

RfbD has been extensively investigated in Salmonella enterica. The crystal structure has been obtained, a color based enzyme assay has been developed, Mg2+ and NADPH dependence for the reaction has been determined [Giraud99, Graninger99, Stern99, Blankenfeldt02].

Gene Citations: [Yao94, Bastin95]

Locations: cytosol

Map Position: [2,109,101 <- 2,110,000] (45.46 centisomes)
Length: 900 bp / 299 aa

Molecular Weight of Polypeptide: 32.694 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006764 , CGSC:295 , EchoBASE:EB2310 , EcoGene:EG12411 , EcoliWiki:b2040 , ModBase:P37760 , OU-Microarray:b2040 , PortEco:rfbD , PR:PRO_000023730 , Pride:P37760 , Protein Model Portal:P37760 , RefSeq:NP_416544 , RegulonDB:EG12411 , SMR:P37760 , String:511145.b2040 , Swiss-Model:P37760 , UniProt:P37760

Relationship Links: InterPro:IN-FAMILY:IPR005913 , InterPro:IN-FAMILY:IPR016040 , Pfam:IN-FAMILY:PF04321

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA]
GO:0009243 - O antigen biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0019305 - dTDP-rhamnose biosynthetic process Inferred by computational analysis [UniProtGOA12]
GO:0045226 - extracellular polysaccharide biosynthetic process Inferred by computational analysis [GOA01a, GOA]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008831 - dTDP-4-dehydrorhamnose reductase activity Inferred by computational analysis [GOA01, GOA01a, GOA]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]

MultiFun Terms: cell structure surface antigens (ECA, O antigen of LPS)
metabolism biosynthesis of macromolecules (cellular constituents) lipopolysaccharide O antigen
metabolism central intermediary metabolism sugar nucleotide biosynthesis, conversions

Essentiality data for rfbD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 30-Jul-2013 by Kubo A , SRI International


Enzymatic reaction of: dTDP-4-dehydrorhamnose reductase

Synonyms: dTDP-4-keto-L-rhamnose reductase, dTDP-6-deoxy-L-mannose dehydrogenase, dTDP-L-rhamnose synthetase, dTDP-6-deoxy-L-mannose:NADP+ 4-oxidoreductase

EC Number: 1.1.1.133

dTDP-β-L-rhamnose + NADP+ <=> dTDP-4-dehydro-β-L-rhamnose + NADPH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the opposite direction.

In Pathways: O-antigen building blocks biosynthesis (E. coli) , dTDP-L-rhamnose biosynthesis I


Subunit of: dTDP-L-rhamnose synthetase

Synonyms: dTDP-L-rhamnose synthetase complex

Subunit composition of dTDP-L-rhamnose synthetase = [RfbC][RfbD]
         dTDP-4-dehydrorhamnose 3,5-epimerase = RfbC (extended summary available)
         dTDP-4-dehydrorhamnose reductase = RfbD (extended summary available)


Enzymatic reaction of: dTDP-L-rhamnose synthetase

EC Number: 1.1.1.-

dTDP-β-L-rhamnose + NAD+ <=> dTDP-4-dehydro-6-deoxy-α-D-glucopyranose + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

This reaction is reversible.

In Pathways: O-antigen building blocks biosynthesis (E. coli) , dTDP-L-rhamnose biosynthesis I

pH(opt): 7.5 [BRENDA14, Wahl79]


Sequence Features

Feature Class Location Citations Comment
Nucleotide-Phosphate-Binding-Region 7 -> 11
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 11 -> 12
[UniProt10]
UniProt: NADP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 12
[UniProt10]
UniProt: NAD; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 30 -> 31
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 39 -> 40
[UniProt10]
UniProt: NAD/NADP; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 62 -> 65
[UniProt10]
UniProt: NAD; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 63 -> 65
[UniProt10]
UniProt: NADP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 102
[UniProt10]
UniProt: NADP; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Protein-Segment 104 -> 105
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;
Nucleotide-Phosphate-Binding-Region 128 -> 132
[UniProt10]
UniProt: NAD/NADP; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 153
[UniProt10]
UniProt: Substrate; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 154
[UniProt10]
UniProt: NAD; via amide nitrogen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 223
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 260
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Tue May 13, 1997:
test 11


10/20/97 Gene b2040 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12411; confirmed by SwissProt match.


References

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bastin95: Bastin DA, Reeves PR (1995). "Sequence and analysis of the O antigen gene (rfb) cluster of Escherichia coli O111." Gene 1995;164(1);17-23. PMID: 7590310

Blankenfeldt02: Blankenfeldt W, Kerr ID, Giraud MF, McMiken HJ, Leonard G, Whitfield C, Messner P, Graninger M, Naismith JH (2002). "Variation on a theme of SDR. dTDP-6-deoxy-L- lyxo-4-hexulose reductase (RmlD) shows a new Mg2+-dependent dimerization mode." Structure 10(6);773-86. PMID: 12057193

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

Giraud00: Giraud MF, Naismith JH (2000). "The rhamnose pathway." Curr Opin Struct Biol 10(6);687-96. PMID: 11114506

Giraud99: Giraud MF, McMiken HJ, Leonard GA, Messner P, Whitfield C, Naismith JH (1999). "Overexpression, purification, crystallization and preliminary structural study of dTDP-6-deoxy-L-lyxo-4-hexulose reductase (RmlD), the fourth enzyme of the dTDP-L-rhamnose synthesis pathway, from Salmonella enterica serovar Typhimurium." Acta Crystallogr D Biol Crystallogr 55(Pt 12);2043-6. PMID: 10666586

Glaser72: Glaser L "Epimerases." Academic Press, New York 1972;Third:355-380.

GOA: GOA "Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity."

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Graninger99: Graninger M, Nidetzky B, Heinrichs DE, Whitfield C, Messner P (1999). "Characterization of dTDP-4-dehydrorhamnose 3,5-epimerase and dTDP-4-dehydrorhamnose reductase, required for dTDP-L-rhamnose biosynthesis in Salmonella enterica serovar Typhimurium LT2." J Biol Chem 274(35);25069-77. PMID: 10455186

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Stern99: Stern RJ, Lee TY, Lee TJ, Yan W, Scherman MS, Vissa VD, Kim SK, Wanner BL, McNeil MR (1999). "Conversion of dTDP-4-keto-6-deoxyglucose to free dTDP-4-keto-rhamnose by the rmIC gene products of Escherichia coli and Mycobacterium tuberculosis." Microbiology 1999;145 ( Pt 3);663-71. PMID: 10217500

Stevenson94: Stevenson G, Neal B, Liu D, Hobbs M, Packer NH, Batley M, Redmond JW, Lindquist L, Reeves P (1994). "Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster." J Bacteriol 1994;176(13);4144-56. PMID: 7517391

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Wahl79: Wahl HP, Grisebach H (1979). "Biosynthesis of streptomycin. dTDP-dihydrostreptose synthase from Streptomyces griseus and dTDP-4-keto-L-rhamnose 3,5-epimerase from S. griseus and Escherichia coli Y10." Biochim Biophys Acta 568(1);243-52. PMID: 109125

Webb92: Webb EC "Enzyme Nomenclature 1992." Academic Press, Inc., San Diego, 1992.

Yao94: Yao Z, Valvano MA (1994). "Genetic analysis of the O-specific lipopolysaccharide biosynthesis region (rfb) of Escherichia coli K-12 W3110: identification of genes that confer group 6 specificity to Shigella flexneri serotypes Y and 4a." J Bacteriol 1994;176(13);4133-43. PMID: 7517390


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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Fri Dec 19, 2014, BIOCYC14A.