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Escherichia coli K-12 substr. MG1655 Enzyme: L-ribulose 5-phosphate 4-epimerase



Gene: ulaF Accession Numbers: G7860 (EcoCyc), b4198, ECK4194

Synonyms: yjfX, sgaE

Regulation Summary Diagram: ?

Summary:
L-ribulose 5-phosphate 4-epimerase is an enzyme in the pathway of anaerobic L-ascorbate degradation [Yew02].

UlaF: "utilization of L-ascorbate" [Yew02]

Gene Citations: [Campos02]

Locations: cytosol

Map Position: [4,421,723 -> 4,422,409] (95.3 centisomes)
Length: 687 bp / 228 aa

Molecular Weight of Polypeptide: 25.278 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013734 , DIP:DIP-10868N , EchoBASE:EB2391 , EcoGene:EG12498 , EcoliWiki:b4198 , Mint:MINT-1288465 , ModBase:P39306 , OU-Microarray:b4198 , PortEco:ulaF , PR:PRO_000024180 , Protein Model Portal:P39306 , RefSeq:NP_418619 , RegulonDB:G7860 , SMR:P39306 , String:511145.b4198 , Swiss-Model:P39306 , UniProt:P39306

Relationship Links: InterPro:IN-FAMILY:IPR001303 , InterPro:IN-FAMILY:IPR023499 , Pfam:IN-FAMILY:PF00596 , Smart:IN-FAMILY:SM01007

In Paralogous Gene Group: 450 (4 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0019852 - L-ascorbic acid metabolic process Inferred from experiment Inferred by computational analysis [GOA06, Campos04]
GO:0019854 - L-ascorbic acid catabolic process Inferred by computational analysis [UniProtGOA12]
Molecular Function: GO:0008742 - L-ribulose-phosphate 4-epimerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Yew02]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA06]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism central intermediary metabolism unassigned reversible reactions

Essentiality data for ulaF 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 ? 10-Nov-2008 by Keseler I , SRI International


Enzymatic reaction of: L-ribulose 5-phosphate 4-epimerase

EC Number: 5.1.3.4

L-ribulose 5-phosphate <=> D-xylulose 5-phosphate

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

This reaction is reversible.

In Pathways: L-ascorbate degradation I (bacterial, anaerobic)

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
L-ribulose 5-phosphate
95.0
[Lee68, BRENDA14]
L-ribulose 5-phosphate
47.0
1.1, 19.4
[Samuel01, BRENDA14]
L-ribulose 5-phosphate
60.0, 87.0
20.4, 20.7, 22.4
[Johnson98b, BRENDA14]
L-ribulose 5-phosphate
47.1, 110.0, 415.0, 493.0
0.5, 6.08, 17.3, 21.8, 36.5
[Lee00c, BRENDA14]

pH(opt): 7 [BRENDA14, Lee68]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 74
[UniProt10a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 93
[UniProt10a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 95
[UniProt10a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 167
[UniProt10a]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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

Campos02: Campos E, Aguilar J, Baldoma L, Badia J (2002). "The gene yjfQ encodes the repressor of the yjfR-X regulon (ula), which is involved in L-ascorbate metabolism in Escherichia coli." J Bacteriol 184(21);6065-8. PMID: 12374842

Campos04: Campos E, Baldoma L, Aguilar J, Badia J (2004). "Regulation of expression of the divergent ulaG and ulaABCDEF operons involved in LaAscorbate dissimilation in Escherichia coli." J Bacteriol 186(6);1720-8. PMID: 14996803

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, 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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Johnson98b: Johnson AE, Tanner ME (1998). "Epimerization via carbon-carbon bond cleavage. L-ribulose-5-phosphate 4-epimerase as a masked class II aldolase." Biochemistry 37(16);5746-54. PMID: 9548961

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

Lee00c: Lee LV, Poyner RR, Vu MV, Cleland WW (2000). "Role of metal ions in the reaction catalyzed by L-ribulose-5-phosphate 4-epimerase." Biochemistry 39(16);4821-30. PMID: 10769139

Lee68: Lee N, Patrick JW, Masson M (1968). "Crystalline L-ribulose 5-phosphate 4-epimerase from Escherichia coli." J Biol Chem 1968;243(18);4700-5. PMID: 4879898

Samuel01: Samuel J, Luo Y, Morgan PM, Strynadka NC, Tanner ME (2001). "Catalysis and binding in L-ribulose-5-phosphate 4-epimerase: a comparison with L-fuculose-1-phosphate aldolase." Biochemistry 40(49);14772-80. PMID: 11732896

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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."

Yew02: Yew WS, Gerlt JA (2002). "Utilization of L-ascorbate by Escherichia coli K-12: assignments of functions to products of the yjf-sga and yia-sgb operons." J Bacteriol 2002;184(1);302-6. PMID: 11741871

Other References Related to Gene Regulation

Zhang03a: Zhang Z, Aboulwafa M, Smith MH, Saier MH (2003). "The ascorbate transporter of Escherichia coli." J Bacteriol 185(7);2243-50. PMID: 12644495


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 Fri Nov 28, 2014, BIOCYC13B.