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Escherichia coli K-12 substr. MG1655 Enzyme: dTDP-4-dehydrorhamnose 3,5-epimerase



Gene: rfbC Accession Numbers: EG11979 (EcoCyc), b2038, ECK2032

Synonyms: rfbD, rmlC

Regulation Summary Diagram: ?

Component of: dTDP-L-rhamnose synthetase

Summary:
dTDP-4-dehydrorhamnose 3,5-epimerase 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, which is known as dTDP-L-rhamnose synthetase. The epimerase catalyzes inversion at C-3 and C-5 via corresponding enediols, but these molecules cannot be released from the enzyme. The reductase then catalyzes the stereospecific reduction of the 4-keto group of epimerase-bound dTDP-4-dehydro-6-deoxy-L-mannose. [Stern99, Webb92, Glaser72]

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]

dTDP-4-dehydrorhamnose 3,5-epimerase is coded for by the rfbC gene. [Yao94] rfbC was identified in a screen for genes that reduce the lethal effects of stress. An rfbC insertion mutant is more sensitive than wild type to mitomycin C and other stresses [Han10].

The crystal structure of the epimerase in Salmonella enterica was resolved to 2.17 Å resolution [Giraud99].

Gene Citations: [Bastin95]

Locations: cytosol

Map Position: [2,107,605 <- 2,108,162] (45.43 centisomes)
Length: 558 bp / 185 aa

Molecular Weight of Polypeptide: 21.27 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006759 , CGSC:38129 , DIP:DIP-10681N , EchoBASE:EB1922 , EcoGene:EG11979 , EcoliWiki:b2038 , Mint:MINT-1257696 , ModBase:P37745 , OU-Microarray:b2038 , PortEco:rfbC , PR:PRO_000023729 , Pride:P37745 , Protein Model Portal:P37745 , RefSeq:NP_416542 , RegulonDB:EG11979 , SMR:P37745 , String:511145.b2038 , Swiss-Model:P37745 , UniProt:P37745

Relationship Links: InterPro:IN-FAMILY:IPR000888 , InterPro:IN-FAMILY:IPR011051 , InterPro:IN-FAMILY:IPR014710 , Panther:IN-FAMILY:PTHR21047 , Pfam:IN-FAMILY:PF00908 , ProDom:IN-FAMILY:PD001462

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006974 - cellular response to DNA damage stimulus Inferred from experiment [Han10]
GO:0046677 - response to antibiotic Inferred from experiment [Han10]
GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProtGOA11a, GOA01a, 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 [GOA]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Arifuzzaman06, Butland05]
GO:0008830 - dTDP-4-dehydrorhamnose 3,5-epimerase activity Inferred by computational analysis [GOA01, GOA01a, GOA]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm

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 rfbC 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 3,5-epimerase

Synonyms: dTDP-4-keto-6-deoxyglucose 3,5-epimerase, TDP-4-keto-L-rhamnose-3,5-epimerase, dTDP-4-dehydro-6-deoxy-D-glucose 3,5-epimerase

EC Number: 5.1.3.13

dTDP-4-dehydro-6-deoxy-α-D-glucopyranose <=> dTDP-4-dehydro-β-L-rhamnose

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 direction shown.

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

Citations: [Stern99]


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
Amino-Acid-Sites-That-Bind 23
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 28
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 47
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 49
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 59
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 62
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 72
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 83
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 119
[UniProt10]
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 132
[UniProt10]
UniProt: May have a key role in proton donation to C5'; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity;
Protein-Segment 168 -> 169
[UniProt10]
UniProt: Substrate binding; Sequence Annotation Type: region of interest; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b2038 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11979; confirmed by SwissProt match.


References

Arifuzzaman06: Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

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

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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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

Giraud99: Giraud MF, Gordon FM, Whitfield C, Messner P, McMahon SA, Naismith JH (1999). "Purification, crystallization and preliminary structural studies of dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (RmlC), the third enzyme of the dTDP-L-rhamnose synthesis pathway, from Salmonella enterica serovar typhimurium." Acta Crystallogr D Biol Crystallogr 55(Pt 3);706-8. PMID: 10089454

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."

Han10: Han X, Dorsey-Oresto A, Malik M, Wang JY, Drlica K, Zhao X, Lu T (2010). "Escherichia coli genes that reduce the lethal effects of stress." BMC Microbiol 10;35. PMID: 20128927

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

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

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

Other References Related to Gene Regulation

Zaslaver06: Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U (2006). "A comprehensive library of fluorescent transcriptional reporters for Escherichia coli." Nat Methods 3(8);623-8. PMID: 16862137


Report Errors or Provide Feedback
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 Thu Nov 27, 2014, biocyc13.