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

Gene: rhaA Accession Numbers: EG11867 (EcoCyc), b3903, ECK3896

Regulation Summary Diagram: ?

Regulation summary diagram for rhaA

Subunit composition of L-rhamnose isomerase = [RhaA]4
         L-rhamnose isomerase = RhaA

L-rhamnose isomerase catalyzes the first step in the utilization of the deoxyhexose sugar rhamnose.

L-rhamnose isomerase is also capable of using L-lyxose as a substrate. With L-lyxose isomerase activity and activation of L-xylulose kinase, E. coli is able to metabolize the uncommon sugar, L-lyxose [Badia91, Sanchez94].

Crystal structures of L-rhamnose isomerase have been determined. Despite low sequence similarity, the enzyme shows structural similarity to xylose isomerase from Streptomyces rubiginosus. The data suggests the possibility of a metal-mediated hydride shift reaction mechanism [Korndorfer00].

Expression of rhaA is induced by L-rhamnose [Badia91, Moralejo93]. L-lyxose can also induce expression of RhaA [Badia91].

rhaA mutants can not utilize rhamnose as a source of carbon [Power67].

Gene Citations: [Egan94, Via96]

Locations: cytosol

Map Position: [4,092,746 <- 4,094,005] (88.21 centisomes, 318°)
Length: 1260 bp / 419 aa

Molecular Weight of Polypeptide: 47.199 kD (from nucleotide sequence), 47.0 kD (experimental) [Badia89 ]

Molecular Weight of Multimer: 188.0 kD (experimental) [Korndorfer00]

pI: 5.78

Unification Links: ASAP:ABE-0012736 , CGSC:292 , DIP:DIP-10690N , DisProt:DP00429 , EchoBASE:EB1813 , EcoGene:EG11867 , EcoliWiki:b3903 , ModBase:P32170 , OU-Microarray:b3903 , PortEco:rhaA , PR:PRO_000023733 , Pride:P32170 , Protein Model Portal:P32170 , RefSeq:YP_026276 , RegulonDB:EG11867 , SMR:P32170 , String:511145.b3903 , UniProt:P32170

Relationship Links: InterPro:IN-FAMILY:IPR009308 , InterPro:IN-FAMILY:IPR013022 , PDB:Structure:1D8W , PDB:Structure:1DE5 , PDB:Structure:1DE6 , Pfam:IN-FAMILY:PF06134

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for rhaA

GO Terms:

Biological Process: GO:0019301 - rhamnose catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, Power67]
GO:0019324 - L-lyxose metabolic process Inferred from experiment [Badia91]
GO:0019299 - rhamnose metabolic process Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
Molecular Function: GO:0008740 - L-rhamnose isomerase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Badia91]
GO:0042802 - identical protein binding Inferred from experiment [Korndorfer00]
GO:0016853 - isomerase activity Inferred by computational analysis [UniProtGOA11a]
GO:0030145 - manganese ion binding Inferred by computational analysis [GOA06, GOA01a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Created 27-Nov-2007 by Keseler I , SRI International
Last-Curated ? 28-Nov-2007 by Keseler I , SRI International

Enzymatic reaction of: L-rhamnose isomerase

Synonyms: L-rhamnose ketol-isomerase

EC Number:

β-L-rhamnopyranose <=> keto-L-rhamnulose

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. [Takagi64a]

Alternative Substrates [Comment 1]:

In Pathways: superpathway of fucose and rhamnose degradation , L-rhamnose degradation I

The enzyme was first purified from E. coli B [Takagi64a].

Cofactors or Prosthetic Groups: Mn2+ [Takagi64a]

Inhibitors (Unknown Mechanism): L-rhamnitol [Korndorfer00] , p-chloromercuribenzoate [Takagi64a, Comment 2] , EDTA [Takagi64a]

Kinetic Parameters:

Km (μM)

pH(opt): 7.6 [Takagi64a]

Enzymatic reaction of: L-lyxose isomerase (L-rhamnose isomerase)

EC Number: 5.1.3.-

β-L-lyxopyranose <=> L-xylulose

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: L-lyxose degradation

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of L-rhamnose isomerase with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 226
UniProt: Zinc.
Metal-Binding-Site 259
UniProt: Zinc.
Metal-Binding-Site 262
UniProt: Manganese.
Metal-Binding-Site 286
UniProt: Zinc.
Metal-Binding-Site 294
UniProt: Manganese.
Metal-Binding-Site 296
UniProt: Manganese.
Metal-Binding-Site 326
UniProt: Zinc.
Sequence-Conflict 359 -> 360
[Plunkett93, UniProt10]
UniProt: (in Ref. 2; AAB03036);
Sequence-Conflict 366
[Moralejo93, UniProt10]
UniProt: (in Ref. 1; CAA43002);

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3903 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11867; confirmed by SwissProt match.


Badia89: Badia J, Baldoma L, Aguilar J, Boronat A (1989). "Identification of the rhaA, rhaB and rhaD gene products from Escherichia coli K-12." FEMS Microbiol Lett 53(3);253-7. PMID: 2558952

Badia91: Badia J, Gimenez R, Baldoma L, Barnes E, Fessner WD, Aguilar J (1991). "L-lyxose metabolism employs the L-rhamnose pathway in mutant cells of Escherichia coli adapted to grow on L-lyxose." J Bacteriol 1991;173(16);5144-50. PMID: 1650346

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

Egan94: Egan SM, Schleif RF (1994). "DNA-dependent renaturation of an insoluble DNA binding protein. Identification of the RhaS binding site at rhaBAD." J Mol Biol 1994;243(5);821-9. PMID: 7966303

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."

Korndorfer00: Korndorfer IP, Fessner WD, Matthews BW (2000). "The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution." J Mol Biol 300(4);917-33. PMID: 10891278

Moralejo93: Moralejo P, Egan SM, Hidalgo E, Aguilar J (1993). "Sequencing and characterization of a gene cluster encoding the enzymes for L-rhamnose metabolism in Escherichia coli." J Bacteriol 175(17);5585-94. PMID: 8396120

Plunkett93: Plunkett G, Burland V, Daniels DL, Blattner FR (1993). "Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes." Nucleic Acids Res 1993;21(15);3391-8. PMID: 8346018

Power67: Power J (1967). "The L-rhamnose genetic system in Escherichia coli K-12." Genetics 55(3);557-68. PMID: 5341476

Sanchez94: Sanchez JC, Gimenez R, Schneider A, Fessner WD, Baldoma L, Aguilar J, Badia J (1994). "Activation of a cryptic gene encoding a kinase for L-xylulose opens a new pathway for the utilization of L-lyxose by Escherichia coli." J Biol Chem 1994;269(47);29665-9. PMID: 7961955

Takagi64a: Takagi Y, Sawada H (1964). "The metabolism of L-rhamnose in Escherichia coli. I. L-rhamnose isomerase." Biochim Biophys Acta 92:10-17. PMID: 14243758

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

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."

Via96: Via P, Badia J, Baldoma L, Obradors N, Aguilar J (1996). "Transcriptional regulation of the Escherichia coli rhaT gene." Microbiology 1996;142 ( Pt 7);1833-40. PMID: 8757746

Other References Related to Gene Regulation

Bhende99: Bhende PM, Egan SM (1999). "Amino acid-DNA contacts by RhaS: an AraC family transcription activator." J Bacteriol 181(17);5185-92. PMID: 10464186

Egan93: Egan SM, Schleif RF (1993). "A regulatory cascade in the induction of rhaBAD." J Mol Biol 1993;234(1);87-98. PMID: 8230210

Holcroft00: Holcroft CC, Egan SM (2000). "Roles of cyclic AMP receptor protein and the carboxyl-terminal domain of the alpha subunit in transcription activation of the Escherichia coli rhaBAD operon." J Bacteriol 182(12);3529-35. PMID: 10852886

Holcroft00a: Holcroft CC, Egan SM (2000). "Interdependence of activation at rhaSR by cyclic AMP receptor protein, the RNA polymerase alpha subunit C-terminal domain, and rhaR." J Bacteriol 2000;182(23);6774-82. PMID: 11073923

Wickstrum04: Wickstrum JR, Egan SM (2004). "Amino acid contacts between sigma 70 domain 4 and the transcription activators RhaS and RhaR." J Bacteriol 186(18);6277-85. PMID: 15342598

Wickstrum05: Wickstrum JR, Santangelo TJ, Egan SM (2005). "Cyclic AMP receptor protein and RhaR synergistically activate transcription from the L-rhamnose-responsive rhaSR promoter in Escherichia coli." J Bacteriol 187(19);6708-18. PMID: 16166533

Wickstrum07: Wickstrum JR, Skredenske JM, Kolin A, Jin DJ, Fang J, Egan SM (2007). "Transcription activation by the DNA-binding domain of the AraC family protein RhaS in the absence of its effector-binding domain." J Bacteriol 189(14);4984-93. PMID: 17513476

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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