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Escherichia coli K-12 substr. MG1655 Enzyme: rhamnulose-1-phosphate aldolase

Gene: rhaD Accession Numbers: EG11866 (EcoCyc), b3902, ECK3895

Regulation Summary Diagram

Regulation summary diagram for rhaD

Subunit composition of rhamnulose-1-phosphate aldolase = [RhaD]4
         rhamnulose-1-phosphate aldolase monomer = RhaD

Rhamnulose-1-phosphate aldolase is a class II aldolase that catalyzes the third step in the L-rhamnose degradation pathway.

The enzyme contains 2 molecules of zinc per enzyme complex [Schwartz72]. If cobalt or selected other divalent metal ions are artificially substituted for zinc, the enzyme has an oxygenase activity in the presence of dihydroxyacetone phosphate [Hixon96].

The enzyme has been crystallized [Chiu69, Schwartz74], and crystal structures have been solved [Kroemer02, Kroemer03]. A catalytic mechanism was proposed based on results from site-directed mutagenesis in combination with structural information [Kroemer03]. Anisotropic mobility of the N-terminal "antenna domain" supports catalysis [Grueninger08]. Stereospecificity of RhaD has been investigated [Schoevaart00].

RhaD (there called Rua) was used in a study of designed protein-protein associations; certain mutations generated a new contact surface and allowed formation of an octamer [Grueninger08a].

Expression of RhaD is induced by L-rhamnose as well as L-lyxose [Badia91].

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

Gene Citations: [Egan94, Via96, Moralejo93]

Locations: cytosol

Map Position: [4,091,471 <- 4,092,295] (88.18 centisomes, 317°)
Length: 825 bp / 274 aa

Molecular Weight of Polypeptide: 30.145 kD (from nucleotide sequence), 32.0 kD (experimental) [Badia89]

Molecular Weight of Multimer: 135.0 kD (experimental) [Chiu69]

pI: 5.88

Unification Links: ASAP:ABE-0012731, CGSC:289, EchoBASE:EB1812, EcoGene:EG11866, EcoliWiki:B3902, ModBase:P32169, OU-Microarray:b3902, PortEco:rhaD, PR:PRO_000023735, Protein Model Portal:P32169, RefSeq:NP_418338, RegulonDB:EG11866, SMR:P32169, String:511145.b3902, UniProt:P32169

Relationship Links: InterPro:IN-FAMILY:IPR001303, InterPro:IN-FAMILY:IPR013447, PDB:Structure:1GT7, PDB:Structure:1OJR, PDB:Structure:2UYU, PDB:Structure:2UYV, PDB:Structure:2V9O, PDB:Structure:2V29, PDB:Structure:2V2A, PDB:Structure:2V2B, PDB:Structure:2V9E, PDB:Structure:2V9F, PDB:Structure:2V9G, PDB:Structure:2V9I, PDB:Structure:2V9L, PDB:Structure:2V9M, PDB:Structure:2V9N, Pfam:IN-FAMILY:PF00596, Smart:IN-FAMILY:SM01007

Gene-Reaction Schematic

Gene-Reaction Schematic

Genetic Regulation Schematic

Genetic regulation schematic for rhaD

GO Terms:
Biological Process:
Inferred from experimentInferred by computational analysisGO:0019301 - rhamnose catabolic process [UniProtGOA12, GOA01a, Power67]
Inferred by computational analysisGO:0019299 - rhamnose metabolic process [UniProtGOA11a, GOA06]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0008994 - rhamnulose-1-phosphate aldolase activity [GOA06, GOA01, GOA01a, Chiu69]
Inferred from experimentGO:0042802 - identical protein binding [Chiu69]
Inferred by computational analysisGO:0016829 - lyase activity [UniProtGOA11a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Cellular Component:
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06]
Inferred by computational analysisGO:0005829 - cytosol [DiazMejia09]

MultiFun Terms: metabolismcarbon utilizationcarbon compounds

Last-Curated 21-Feb-2008 by Keseler I, SRI International

Enzymatic reaction of: rhamnulose-1-phosphate aldolase

Inferred from experiment

Synonyms: L-rhamnulose-1-phosphate lactaldehyde-lyase, RhuA

EC Number:

L-rhamnulose 1-phosphate ⇄ (S)-lactaldehyde + glycerone phosphate

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction of enzyme catalysis.

This reaction is reversible. [Chiu69]

Alternative Substrates for L-rhamnulose 1-phosphate [Chiu75]: L-xylulose 1-phosphate, keto-D-sorbose 1-phosphate
Alternative Substrates for (S)-lactaldehyde [Chiu75]: (R)-lactaldehyde [Chiu65, Chiu69], formaldehyde [Chiu69, Chiu65], acetaldehyde [Chiu69, Chiu65], glycolaldehyde [Chiu69, Chiu65], D-glyceraldehyde [Chiu69, Chiu65]

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

The enzyme was first partially purified from E. coli B [Sawada64]. Other researchers used E. coli K40, a K12 derivative [Chiu65, Chiu69].

At equilibrium, the reaction mixture contains approximately 75% L-rhamnulose-1-phosphate [Chiu69].

The Km for L-xylulose-1-phosphate is 200 µM and that for D-sorbose-1-phosphate is 1.8 mM [Chiu69].

Cofactors or Prosthetic Groups: Zn2+ [Schwartz74, Schwartz72, GarciaJunceda95], K+ [Comment 1, Chiu69]

Inhibitors (Competitive): L-rhamnitol 1-phosphate [Chiu75], o-phenanthroline [Chiu75], Li+ [Chiu69, Comment 2] Inhibitors (Unknown Mechanism): Hg2+ [Chiu75], 8-hydroxyquinoline-5-sulfonic acid [Chiu75, Schwartz72], p-mercuribenzoate [Chiu75, Schwartz72a], 2,2'-dipyridyl [Chiu75], EDTA [Schwartz72, Comment 3]Kinetic Parameters:
Substrate Km (μM) kcat (sec-1) kcat/Km (sec-1 μM-1) Citations
L-rhamnulose 1-phosphate 10000.0 [Sawada64, BRENDA14]
L-rhamnulose 1-phosphate 300.0 38.3 0.13 [Chiu69, BRENDA14]
glycerone phosphate 3000.0 [Chiu69]
glycerone phosphate 9.1 [Jimenez09, BRENDA14]
(S)-lactaldehyde 6000.0 [Chiu69]

pH(opt): 9.3 [BRENDA14, Sawada64], 7.5 [Chiu69]

Sequence Features

Protein sequence of rhamnulose-1-phosphate aldolase monomer with features indicated

Feature Class Location Citations Comment
Pfam PF00596 12 -> 238
Inferred by computational analysis[Finn14]
Aldolase_II : Class II Aldolase and Adducin N-terminal domain
Active-Site 117
Author statement[UniProt15]
Metal-Binding-Site 141
Author statement[UniProt15]
UniProt: Zinc.
Metal-Binding-Site 143
Author statement[UniProt15]
UniProt: Zinc.
Metal-Binding-Site 212
Author statement[UniProt15]
UniProt: Zinc.

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Units

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3902 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11866; 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

BRENDA14: BRENDA team (2014). Imported from BRENDA version existing on Aug 2014.

Chiu65: Chiu TH, Feingold DS (1965). "Substrate specificity of L-rhamnulose 1-phosphate aldolase." Biochem Biophys Res Commun 19;511-6. PMID: 14339000

Chiu69: Chiu TH, Feingold DS (1969). "L-rhamnulose 1-phosphate aldolase from Escherichia coli. Crystallization and properties." Biochemistry 1969;8(1);98-108. PMID: 4975916

Chiu75: Chiu TH, Evans KL, Feingold DS (1975). "L-Rhamnulose-1-phosphate aldosase." Methods Enzymol 1975;42;364-9. PMID: 237196

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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

GarciaJunceda95: Garcia-Junceda E, Shen GJ, Sugai T, Wong CH (1995). "A new strategy for the cloning, overexpression and one step purification of three DHAP-dependent aldolases: rhamnulose-1-phosphate aldolase, fuculose-1-phosphate aldolase and tagatose-1,6-diphosphate aldolase." Bioorg Med Chem 3(7);945-53. PMID: 7582972

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."

Grueninger08: Grueninger D, Schulz GE (2008). "Antenna domain mobility and enzymatic reaction of L-rhamnulose-1-phosphate aldolase." Biochemistry 47(2);607-14. PMID: 18085797

Grueninger08a: Grueninger D, Treiber N, Ziegler MO, Koetter JW, Schulze MS, Schulz GE (2008). "Designed protein-protein association." Science 319(5860);206-9. PMID: 18187656

Hixon96: Hixon M, Sinerius G, Schneider A, Walter C, Fessner WD, Schloss JV (1996). "Quo vadis photorespiration: a tale of two aldolases." FEBS Lett 392(3);281-4. PMID: 8774862

Jimenez09: Jimenez A, Clapes P, Crehuet R (2009). "Protein flexibility and metal coordination changes in DHAP-dependent aldolases." Chemistry 15(6);1422-8. PMID: 19115296

Kroemer02: Kroemer M, Schulz GE (2002). "The structure of L-rhamnulose-1-phosphate aldolase (class II) solved by low-resolution SIR phasing and 20-fold NCS averaging." Acta Crystallogr D Biol Crystallogr 58(Pt 5);824-32. PMID: 11976494

Kroemer03: Kroemer M, Merkel I, Schulz GE (2003). "Structure and catalytic mechanism of L-rhamnulose-1-phosphate aldolase." Biochemistry 42(36);10560-8. PMID: 12962479

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

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

Sawada64: Sawada H, Takagi Y (1964). "The metabolism of L-rhamnose in Escherichia coli. 3. L-rhamnulose-phosphate aldolase." Biochim Biophys Acta 92;26-32. PMID: 14243785

Schoevaart00: Schoevaart R, van Rantwijk F, Sheldon RA (2000). "Stereochemistry of nonnatural aldol reactions catalyzed by DHAP aldolases." Biotechnol Bioeng 70(3);349-52. PMID: 10992239

Schwartz72: Schwartz NB, Feingold DS (1972). "L-rhamnulose 1-phosphate aldolase from Escherichia coli. II. Characterization as a zinc metalloenzyme." Bioinorg Chem 1:233-243.

Schwartz72a: Schwartz NB, Feingold DS (1972). "L-rhamnulose 1-phosphate aldolase from Escherichia coli. III. The role of divalent cations in enzyme activity." Bioinorg Chem 2:75-86.

Schwartz74: Schwartz NB, Abram D, Feingold DS (1974). "L-Rhamnulose 1-phosphate aldolase of Escherichia coli. The role of metal in enzyme structure." Biochemistry 1974;13(8);1726-30. PMID: 4208690

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." 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

Barrios99: Barrios H, Valderrama B, Morett E (1999). "Compilation and analysis of sigma(54)-dependent promoter sequences." Nucleic Acids Res 27(22);4305-13. PMID: 10536136

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

Zhao10b: Zhao K, Liu M, Burgess RR (2010). "Promoter and regulon analysis of nitrogen assimilation factor, sigma54, reveal alternative strategy for E. coli MG1655 flagellar biosynthesis." Nucleic Acids Res 38(4);1273-83. PMID: 19969540

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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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