Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

Escherichia coli K-12 substr. MG1655 Enzyme: L-arabinose isomerase



Gene: araA Accession Numbers: EG10052 (EcoCyc), b0062, ECK0063

Regulation Summary Diagram: ?

Subunit composition of L-arabinose isomerase = [AraA]6
         L-arabinose isomerase monomer = AraA

Summary:
L-arabinose isomerase catalyzes the first step in the degradation of L-arabinose, its isomerization to L-ribulose.

A reaction mechanism was proposed by [Banerjee95]. In vitro, the enzyme can also catalyze the conversion of D-galactose to D-tagatose, which is used commercially as a low-calorie substitute for sucrose [Roh00, Kim01b].

Electron micrographs showed that the subunits of L-arabinose isomerase are arranged in a stack of two trimers [Wallace78]. Crystal structures of the enzyme alone and with a bound Mn2+ ion have been solved; they confirm that the enzyme forms a dimer of trimers [Manjasetty06, Zhu07a].

Most studies of the enzyme and its genetics were done in E. coli B/r. Transcription of the araBAD operon is induced in the presence of L-arabinose by the transcription factor AraC [Casadaban75, Johnson95]. araBAD expression can also induced by L-lyxose [Ibanez00a]. araA mutants can not utilize L-arabinose for growth [Gross59].

Gene Citations: [Ebright85, Reeder91]

Locations: cytosol

Map Position: [66,835 <- 68,337] (1.44 centisomes)
Length: 1503 bp / 500 aa

Molecular Weight of Polypeptide: 56.074 kD (from nucleotide sequence)

Molecular Weight of Multimer: 362.0 kD (experimental) [Patrick69]

pI: 6.27

Unification Links: ASAP:ABE-0000221 , CGSC:1028 , DIP:DIP-9123N , EchoBASE:EB0050 , EcoGene:EG10052 , EcoliWiki:b0062 , ModBase:P08202 , OU-Microarray:b0062 , PortEco:araA , PR:PRO_000022114 , Pride:P08202 , Protein Model Portal:P08202 , RefSeq:NP_414604 , RegulonDB:EG10052 , SMR:P08202 , String:511145.b0062 , UniProt:P08202

Relationship Links: InterPro:IN-FAMILY:IPR003762 , InterPro:IN-FAMILY:IPR004216 , InterPro:IN-FAMILY:IPR009015 , InterPro:IN-FAMILY:IPR024664 , PDB:Structure:2AJT , PDB:Structure:2HXG , PDB:Structure:4F2D , Pfam:IN-FAMILY:PF02610 , Pfam:IN-FAMILY:PF11762 , ProDom:IN-FAMILY:PD018364

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0019568 - arabinose catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Gross59]
GO:0019569 - L-arabinose catabolic process to xylulose 5-phosphate Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA06, De07a]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [UniProtGOA11a]
GO:0005996 - monosaccharide metabolic process Inferred by computational analysis [GOA01a]
GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0008733 - L-arabinose isomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Gross59, Banerjee95]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016861 - intramolecular oxidoreductase activity, interconverting aldoses and ketoses Inferred by computational analysis [GOA01a]
GO:0030145 - manganese ion binding Inferred by computational analysis [GOA06]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [GOA01a]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for araA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]

Credits:
Last-Curated ? 07-Dec-2007 by Keseler I , SRI International


Enzymatic reaction of: L-arabinose isomerase

Synonyms: L-arabinose ketol-isomerase

EC Number: 5.3.1.4

L-arabinopyranose <=> L-ribulose

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.

Alternative Substrates for L-arabinopyranose: β-D-galactose [Kim01b ]

Alternative Substrates for L-ribulose: keto-D-tagatose

In Pathways: L-arabinose degradation I

Summary:
This enzyme was first purified from E. coli B/r [Patrick68, Patrick69, Patrick71].

Cofactors or Prosthetic Groups: Mn2+ [Patrick71, Banerjee95]

Inhibitors (Competitive): ribitol [Patrick68] , L-arabitol [Patrick68]

pH(opt): 7.5 [BRENDA14, Kim04d], 6 [BRENDA14, Patrick75], 6-8 [Patrick68]


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 72
[Lee86, UniProt10b]
Alternate sequence: R → P; UniProt: (in Ref. 1; AAA23463);
Sequence-Conflict 248
[Lee86, UniProt10b]
Alternate sequence: K → E; UniProt: (in Ref. 1; AAA23463);
Metal-Binding-Site 306
[UniProt10a]
UniProt: Manganese;
Metal-Binding-Site 333
[UniProt10a]
UniProt: Manganese;
Metal-Binding-Site 350
[UniProt10a]
UniProt: Manganese;
Sequence-Conflict 360
[Lee86, UniProt10b]
Alternate sequence: A → V; UniProt: (in Ref. 1; AAA23463);
Metal-Binding-Site 450
[UniProt10a]
UniProt: Manganese;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b0062 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10052; confirmed by SwissProt match.


References

Banerjee95: Banerjee S, Anderson F, Farber GK (1995). "The evolution of sugar isomerases." Protein Eng 8(12);1189-95. PMID: 8869631

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

Casadaban75: Casadaban MJ (1975). "Fusion of the Escherichia coli lac genes to the ara promoter: a general technique using bacteriophage Mu-1 insertions." Proc Natl Acad Sci U S A 72(3);809-13. PMID: 1093171

De07a: De Muynck C, Van der Borght J, De Mey M, De Maeseneire SL, Van Bogaert IN, Beauprez J, Soetaert W, Vandamme E (2007). "Development of a selection system for the detection of L-ribose isomerase expressing mutants of Escherichia coli." Appl Microbiol Biotechnol 76(5);1051-7. PMID: 17619876

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

Ebright85: Ebright RH, Beckwith J (1985). "The catabolite gene activator protein (CAP) is not required for indole-3-acetic acid to activate transcription of the araBAD operon of Escherichia coli K-12." Mol Gen Genet 1985;201(1);51-5. PMID: 2997582

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."

Gross59: Gross J, Englesberg E (1959). "Determination of the order of mutational sites governing L-arabinose utilization in Escherichia coli B/r bv transduction with phage Plbt." Virology 9;314-31. PMID: 13829634

Ibanez00a: Ibanez E, Gimenez R, Pedraza T, Baldoma L, Aguilar J, Badia J (2000). "Role of the yiaR and yiaS genes of Escherichia coli in metabolism of endogenously formed L-xylulose." J Bacteriol 2000;182(16);4625-7. PMID: 10913097

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

Johnson95: Johnson CM, Schleif RF (1995). "In vivo induction kinetics of the arabinose promoters in Escherichia coli." J Bacteriol 177(12);3438-42. PMID: 7768852

Kim01b: Kim P, Yoon SH, Roh HJ, Choi JH (2001). "High production of D-tagatose, a potential sugar substitute, using immobilized L-arabinose isomerase." Biotechnol Prog 17(1);208-10. PMID: 11170501

Kim04d: Kim P (2004). "Current studies on biological tagatose production using L-arabinose isomerase: a review and future perspective." Appl Microbiol Biotechnol 65(3);243-9. PMID: 15248040

Lee86: Lee N, Gielow W, Martin R, Hamilton E, Fowler A (1986). "The organization of the araBAD operon of Escherichia coli." Gene 1986;47(2-3);231-44. PMID: 3549454

Manjasetty06: Manjasetty BA, Chance MR (2006). "Crystal structure of Escherichia coli L-arabinose isomerase (ECAI), the putative target of biological tagatose production." J Mol Biol 360(2);297-309. PMID: 16756997

Patrick68: Patrick JW, Lee N (1968). "Purification and properties of an L-arabinose isomerase from Escherichia coli." J Biol Chem 1968;243(16);4312-8. PMID: 4878429

Patrick69: Patrick JW, Lee N (1969). "Subunit structure of L-arabinose isomerase from Escherichia coli." J Biol Chem 244(16);4277-83. PMID: 4896751

Patrick71: Patrick JW, Lee N, Barnes NB, Englesberg E (1971). "Coordination of enzyme synthesis in the L-arabinose operon in Escherichia coli. I. The effect of manganous ion on the synthesis of L-arabinose isomerase." J Biol Chem 246(16);5102-6. PMID: 4936722

Patrick75: Patrick J, Lee N (1975). "L-arabinose isomerase." Methods Enzymol 41;453-8. PMID: 236474

Reeder91: Reeder T, Schleif R (1991). "Mapping, sequence, and apparent lack of function of araJ, a gene of the Escherichia coli arabinose regulon." J Bacteriol 1991;173(24);7765-71. PMID: 1744033

Roh00: Roh HJ, Kim P, Park YC, Choi JH (2000). "Bioconversion of D-galactose into D-tagatose by expression of L-arabinose isomerase." Biotechnol Appl Biochem 31 ( Pt 1);1-4. PMID: 10669396

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt10b: UniProt Consortium (2010). "UniProt version 2010-12 released on 2010-12-01 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."

Wallace78: Wallace LJ, Eiserling FA, Wilcox G (1978). "The shape of L-arabinose isomerase from Escherichia coli." J Biol Chem 1978;253(10);3717-20. PMID: 348696

Zhu07a: Zhu W, Chance MR, Manjasetty B (2007). "Crystal structure of Mn2+-bound Escherichia coli L-arabinose isomerase (ECAI) and implications in protein catalytic mechanism and thermo-stability." Journal of Young Investigators vol. 17.

Other References Related to Gene Regulation

Bustos93: Bustos SA, Schleif RF (1993). "Functional domains of the AraC protein." Proc Natl Acad Sci U S A 90(12);5638-42. PMID: 8516313

Gallegos97: Gallegos MT, Schleif R, Bairoch A, Hofmann K, Ramos JL (1997). "Arac/XylS family of transcriptional regulators." Microbiol Mol Biol Rev 61(4);393-410. PMID: 9409145

Hamilton88: Hamilton EP, Lee N (1988). "Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli." Proc Natl Acad Sci U S A 1988;85(6);1749-53. PMID: 3279415

Huo88: Huo L, Martin KJ, Schleif R (1988). "Alternative DNA loops regulate the arabinose operon in Escherichia coli." Proc Natl Acad Sci U S A 1988;85(15);5444-8. PMID: 3041410

Lee77: Lee N, Carbon J (1977). "Nucleotide sequence of the 5' end of araBAD operon messenger RNA in Escherichia coli B/r." Proc Natl Acad Sci U S A 74(1);49-53. PMID: 189315

Lee81a: Lee NL, Gielow WO, Wallace RG (1981). "Mechanism of araC autoregulation and the domains of two overlapping promoters, Pc and PBAD, in the L-arabinose regulatory region of Escherichia coli." Proc Natl Acad Sci U S A 1981;78(2);752-6. PMID: 6262769

Lee87b: Lee N, Francklyn C, Hamilton EP (1987). "Arabinose-induced binding of AraC protein to araI2 activates the araBAD operon promoter." Proc Natl Acad Sci U S A 1987;84(24);8814-8. PMID: 2962192

Lee89a: Lee DH, Schleif RF (1989). "In vivo DNA loops in araCBAD: size limits and helical repeat." Proc Natl Acad Sci U S A 1989;86(2);476-80. PMID: 2643114

Lee92a: Lee DH, Huo L, Schleif R (1992). "Repression of the araBAD promoter from araO1." J Mol Biol 224(2);335-41. PMID: 1560456

Lisser93: Lisser S, Margalit H (1993). "Compilation of E. coli mRNA promoter sequences." Nucleic Acids Res 21(7);1507-16. PMID: 8479900

Lobell91: Lobell RB, Schleif RF (1991). "AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein." J Mol Biol 218(1);45-54. PMID: 1848302

Niland96: Niland P, Huhne R, Muller-Hill B (1996). "How AraC interacts specifically with its target DNAs." J Mol Biol 264(4);667-74. PMID: 8980677

Reeder93: Reeder T, Schleif R (1993). "AraC protein can activate transcription from only one position and when pointed in only one direction." J Mol Biol 231(2);205-18. PMID: 8510144

Seabold98: Seabold RR, Schleif RF (1998). "Apo-AraC actively seeks to loop." J Mol Biol 278(3);529-38. PMID: 9600836

Smith78: Smith BR, Schleif R (1978). "Nucleotide sequence of the L-arabinose regulatory region of Escherichia coli K12." J Biol Chem 253(19);6931-3. PMID: 357433

Stoltzfus89: Stoltzfus L, Wilcox G (1989). "Effect of mutations in the cyclic AMP receptor protein-binding site on araBAD and araC expression." J Bacteriol 171(2);1178-84. PMID: 2521619

Zhang98d: Zhang X, Schleif R (1998). "Catabolite gene activator protein mutations affecting activity of the araBAD promoter." J Bacteriol 180(2);195-200. PMID: 9440505


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, biocyc12.