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Escherichia coli K-12 substr. MG1655 Enzyme: dTDP-4-dehydro-6-deoxy-D-glucose transaminase



Gene: rffA Accession Numbers: EG11456 (EcoCyc), b3791, ECK3783

Synonyms: rff, fcnA, wecE, yifI

Regulation Summary Diagram: ?

Subunit composition of dTDP-4-dehydro-6-deoxy-D-glucose transaminase = [RffA]4
         dTDP-4-dehydro-6-deoxy-D-glucose transaminase = RffA

Summary:
dTDP-4-dehydro-6-deoxy-D-glucose transaminase is involved in the biosynthesis of enterobacterial common antigen (ECA). This enzyme catalyzes the conversion of TDP-4-keto-6-deoxy-D-glucose to TDP-D-fucosamine. [MeierDieter90, Hwang04].

A Tn10 insertion mutant does not produce ECA [MeierDieter90].

Citations: [Danese98b, Barr93, MeierDieter92]

Locations: cytosol

Map Position: [3,973,169 -> 3,974,299] (85.63 centisomes)
Length: 1131 bp / 376 aa

Molecular Weight of Polypeptide: 41.901 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0012384 , EchoBASE:EB1425 , EcoGene:EG11456 , EcoliWiki:b3791 , ModBase:P27833 , OU-Microarray:b3791 , PortEco:rffA , PR:PRO_000023732 , Pride:P27833 , Protein Model Portal:P27833 , RefSeq:NP_418238 , RegulonDB:EG11456 , SMR:P27833 , String:511145.b3791 , UniProt:P27833

Relationship Links: InterPro:IN-FAMILY:IPR000653 , InterPro:IN-FAMILY:IPR012749 , InterPro:IN-FAMILY:IPR015421 , InterPro:IN-FAMILY:IPR015422 , InterPro:IN-FAMILY:IPR015424 , Pfam:IN-FAMILY:PF01041

In Paralogous Gene Group: 395 (3 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0009246 - enterobacterial common antigen biosynthetic process Inferred from experiment [MeierDieter90]
GO:0009103 - lipopolysaccharide biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0009243 - O antigen biosynthetic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0019180 - dTDP-4-amino-4,6-dideoxygalactose transaminase activity Inferred from experiment Inferred by computational analysis [GOA01a, Hwang04]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11]
GO:0030170 - pyridoxal phosphate binding Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell structure surface antigens (ECA, O antigen of LPS)
metabolism biosynthesis of macromolecules (cellular constituents) enterobacterial common antigen (surface glycolipid)

Essentiality data for rffA 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:
Created 03-Dec-2012 by Keseler I , SRI International
Last-Curated ? 03-Dec-2012 by Keseler I , SRI International


Enzymatic reaction of: dTDP-4-dehydro-6-deoxy-D-glucose transaminase

Synonyms: TDP-4-oxo-6-deoxy-D-glucose transaminase, dTDP-4-oxo-6-deoxy-D-glucose transaminase

EC Number: 2.6.1.59

dTDP-thomosamine + 2-oxoglutarate <=> dTDP-4-dehydro-6-deoxy-α-D-glucopyranose + L-glutamate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible.

Alternative Substrates for L-glutamate: L-glutamine [Hwang04 ]

In Pathways: enterobacterial common antigen biosynthesis , dTDP-N-acetylthomosamine biosynthesis

Cofactors or Prosthetic Groups: pyridoxal 5'-phosphate [Hwang04]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
dTDP-4-dehydro-6-deoxy-α-D-glucopyranose
110.0
0.38
[Hwang04]

T(opt): 37 °C [BRENDA14, Hwang04]

pH(opt): 7.5 [Hwang04]


Sequence Features

Feature Class Location Citations Comment
N6-pyridoxal-phosphate-Lys-Modification 181
[UniProt11a]
UniProt: N6-(pyridoxal phosphate)lysine; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
7/13/1999 (pkarp) Merged genes G349/rffA and EG11456/wecE
10/20/97 Gene b3791 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11456.


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

Barr93: Barr K, Rick PD (1993). "Physical map location of the rffC and rffA genes of Escherichia coli." J Bacteriol 175(17);5738-9. PMID: 8366065

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

Danese98b: Danese PN, Oliver GR, Barr K, Bowman GD, Rick PD, Silhavy TJ (1998). "Accumulation of the enterobacterial common antigen lipid II biosynthetic intermediate stimulates degP transcription in Escherichia coli." J Bacteriol 1998;180(22);5875-84. PMID: 9811644

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

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA01a: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

Hwang04: Hwang BY, Lee HJ, Yang YH, Joo HS, Kim BG (2004). "Characterization and investigation of substrate specificity of the sugar aminotransferase WecE from E. coli K12." Chem Biol 11(7);915-25. PMID: 15271350

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

MeierDieter90: Meier-Dieter U, Starman R, Barr K, Mayer H, Rick PD (1990). "Biosynthesis of enterobacterial common antigen in Escherichia coli. Biochemical characterization of Tn10 insertion mutants defective in enterobacterial common antigen synthesis." J Biol Chem 1990;265(23);13490-7. PMID: 2166030

MeierDieter92: Meier-Dieter U, Barr K, Starman R, Hatch L, Rick PD (1992). "Nucleotide sequence of the Escherichia coli rfe gene involved in the synthesis of enterobacterial common antigen. Molecular cloning of the rfe-rff gene cluster." J Biol Chem 1992;267(2);746-53. PMID: 1730666

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-11 released on 2011-11-22 00:00:00." Database.

UniProtGOA11: 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."

Other References Related to Gene Regulation

Huerta03: Huerta AM, Collado-Vides J (2003). "Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals." J Mol Biol 333(2);261-78. PMID: 14529615

Partridge09: Partridge JD, Bodenmiller DM, Humphrys MS, Spiro S (2009). "NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility." Mol Microbiol 73(4);680-94. PMID: 19656291


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 Sun Nov 23, 2014, biocyc14.