|Gene:||rhaD||Accession Numbers: EG11866 (EcoCyc), b3902, ECK3895|
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].
|Map Position: [4,091,471 <- 4,092,295] (88.18 centisomes)||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]
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
|Biological Process:||GO:0019301 - rhamnose catabolic process
[UniProtGOA12, GOA01, Power67]
GO:0019299 - rhamnose metabolic process [UniProtGOA11, GOA06]
|Molecular Function:||GO:0008994 - rhamnulose-1-phosphate aldolase activity
[GOA06, GOA01a, GOA01, Chiu69]
GO:0042802 - identical protein binding [Chiu69]
GO:0016829 - lyase activity [UniProtGOA11]
GO:0046872 - metal ion binding [UniProtGOA11]
|Cellular Component:||GO:0005737 - cytoplasm
[UniProtGOA11a, UniProtGOA11, GOA06]
GO:0005829 - cytosol [DiazMejia09]
|MultiFun Terms:||metabolism → carbon utilization → carbon compounds|
Enzymatic reaction of: rhamnulose-1-phosphate aldolase
Synonyms: L-rhamnulose-1-phosphate lactaldehyde-lyase, RhuA
EC Number: 18.104.22.168
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. [Chiu69]
Alternative Substrates for (S)-lactaldehyde [Chiu75 ]: (R)-lactaldehyde [Chiu65 , Chiu69 ] , formaldehyde [Chiu69 , Chiu65 ] , acetaldehyde [Chiu69 , Chiu65 ] , glycolaldehyde [Chiu69 , Chiu65 ] , D-glyceraldehyde [Chiu69 , Chiu65 ]
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].
Inhibitors (Unknown Mechanism): Hg2+ [Chiu75] , 8-hydroxyquinoline-5-sulfonic acid [Chiu75, Schwartz72] , p-mercuribenzoate [Chiu75, Schwartz72a] , 2,2'-dipyridyl [Chiu75] , EDTA [Schwartz72, Comment 3]
10/20/97 Gene b3902 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11866; confirmed by SwissProt match.
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
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
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
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
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
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
Zhao10: 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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