Escherichia coli K-12 substr. MG1655 Enzyme: L-rhamnulose kinase

Gene: rhaB Accession Numbers: EG11868 (EcoCyc), b3904, ECK3897

Regulation Summary Diagram: ?

Regulation summary diagram for rhaB

L-rhamnulose kinase catalyzes the second step of rhamnose degradation, the phosphorylation of rhamnulose.

The substrate spectrum of L-rhamnulose kinase has been investigated; the enzyme shows a broad tolerance for structural modifications of the natural substrate [Fessner92]. Rare sugars have been modeled into the active center of the crystal structure [Grueninger07].

L-rhamnulose kinase is a monomer in solution [Grueninger06]. Crystal structures of L-rhamnulose kinase as an apo- and holo-enzyme as well as the ternary complex including the sugar have been determined and show that the enzyme belongs to the hexokinase-hsp70-actin superfamily. A catalytic mechanism has been proposed [Grueninger06].

A mutated form of RhaB has been shown to also phosphorylate L-xylulose to L-xylulose 1-phosphate and to allow growth of E. coli on L-lyxose [Badia91].

The enzyme was first identified in E. coli B [Wilson57].

rhaB mutants are unable to utilize rhamnose as a source of carbon [Power67].

Gene Citations: [Egan94, Via96, Moralejo93]

Locations: cytosol

Map Position: [4,094,002 <- 4,095,471] (88.24 centisomes, 318°)
Length: 1470 bp / 489 aa

Molecular Weight of Polypeptide: 54.069 kD (from nucleotide sequence), 52 kD (experimental) [Badia89 ]

pI: 5.27

Unification Links: ASAP:ABE-0012738 , CGSC:291 , EchoBASE:EB1814 , EcoGene:EG11868 , EcoliWiki:b3904 , ModBase:P32171 , OU-Microarray:b3904 , PortEco:rhaB , PR:PRO_000023734 , Pride:P32171 , Protein Model Portal:P32171 , RefSeq:NP_418340 , RegulonDB:EG11868 , SMR:P32171 , String:511145.b3904 , UniProt:P32171

Relationship Links: InterPro:IN-FAMILY:IPR013449 , InterPro:IN-FAMILY:IPR018484 , InterPro:IN-FAMILY:IPR018485 , PDB:Structure:2CGJ , PDB:Structure:2CGK , PDB:Structure:2CGL , Pfam:IN-FAMILY:PF00370 , Pfam:IN-FAMILY:PF02782

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for rhaB

GO Terms:

Biological Process: GO:0019301 - rhamnose catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA01a, Chiu64, Power67]
GO:0046835 - carbohydrate phosphorylation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Grueninger06]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a, Gaudet10]
GO:0019299 - rhamnose metabolic process Inferred by computational analysis [UniProtGOA11a, GOA06]
Molecular Function: GO:0005524 - ATP binding Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Grueninger06]
GO:0008993 - rhamnulokinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Grueninger06, Fessner92]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0016301 - kinase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016773 - phosphotransferase activity, alcohol group as acceptor Inferred by computational analysis [GOA01a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [Gaudet10]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Curated 16-Mar-2006 by Shearer A , SRI International
Last-Curated ? 28-Nov-2007 by Keseler I , SRI International

Enzymatic reaction of: L-rhamnulose kinase

Synonyms: rhamnulokinase, ATP:L-rhamnulose 1-phosphotransferase, RhuK

EC Number:

L-rhamnulofuranose + ATP <=> L-rhamnulose 1-phosphate + ADP + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction of enzyme catalysis.

The reaction is physiologically favored in the direction shown.

Alternative Substrates for L-rhamnulofuranose [Comment 1 ]: 6-deoxy-D-sorbose [Grueninger07 ] , L-xylulose [Fessner92 ] , D-fructose [Fessner92 ] , L-fuculose [Fessner92 ]

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

Crude extracts were assayed from E. coli B [Wilson57]. The enzyme was partially purified from E. coli K40 [Chiu64] and B [Takagi64] and purified from an unidentified strain of E. coli [Fessner92].

Cofactors or Prosthetic Groups: Mg2+ [Takagi64, Chiu64]

Kinetic Parameters:

Km (μM)

pH(opt): 8.5 [Chiu64]

Sequence Features

Protein sequence of L-rhamnulose kinase with features indicated

Feature Class Location Attached Group Citations Comment
Nucleotide-Phosphate-Binding-Region 13 -> 17 ATP
[Grueninger06, UniProt15]
UniProt: ATP.
Disulfide-Bond-Site 68, 222  
[Grueninger06, UniProt15]
Mutagenesis-Variant 69  
[Grueninger06, UniProt15]
UniProt: Same kinase activity as the wild-type; when associated with A-70 and A-73.
Mutagenesis-Variant 70  
[Grueninger06, UniProt15]
UniProt: Same kinase activity as the wild-type; when associated with A-69 and A-73.
Mutagenesis-Variant 73  
[Grueninger06, UniProt15]
UniProt: Same kinase activity as the wild-type; when associated with A-69 and A-70.
Amino-Acid-Sites-That-Bind 83  
[Grueninger06, UniProt15]
UniProt: Substrate; via amide nitrogen and carbonyl oxygen.
Sequence-Conflict 214  
[Moralejo93, UniProt10]
UniProt: (in Ref. 1; CAA43001);
Protein-Segment 236 -> 238  
[Grueninger06, UniProt15]
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Active-Site 237  
[Grueninger06, UniProt15]
UniProt: Proton acceptor.
Amino-Acid-Sites-That-Bind 259  
[Grueninger06, UniProt15]
UniProt: ATP.
Amino-Acid-Sites-That-Bind 296  
[Grueninger06, UniProt15]
UniProt: Substrate.
Amino-Acid-Sites-That-Bind 304  
[Grueninger06, UniProt15]
UniProt: ATP.
Disulfide-Bond-Site 353, 370  
[Grueninger06, UniProt15]
Sequence-Conflict 388 -> 389  
[Moralejo93, UniProt10]
UniProt: (in Ref. 1; CAA43001);
Amino-Acid-Sites-That-Bind 402  
[Grueninger06, UniProt15]
UniProt: ATP; via amide nitrogen.
Disulfide-Bond-Site 413, 417  

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram


10/20/97 Gene b3904 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11868; 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

Chiu64: Chiu TH, Feingold DS (1964). "The purification and properties of L-rhamnulokinase." Biochim Biophys Acta 92;489-97. PMID: 14264882

Chiu64a: Chiu TH, Feingold D "Purification and properties of L-Rhamnulokinase." B B Acta 1964;92:489-497.

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

Fessner92: Fessner WD, Badia J, Eyrisch O, Schneider A, Sinerius G (1992). "Enzymatic syntheses of rare ketose 1-phosphates." Tetrahedron Letters 33;2231-2234.

Gaudet10: Gaudet P, Livstone M, Thomas P (2010). "Annotation inferences using phylogenetic trees." PMID: 19578431

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."

Grueninger06: Grueninger D, Schulz GE (2006). "Structure and reaction mechanism of L-rhamnulose kinase from Escherichia coli." J Mol Biol 359(3);787-97. PMID: 16674975

Grueninger07: Grueninger D, Schulz GE (2007). "Substrate spectrum of l-rhamnulose kinase related to models derived from two ternary complex structures." FEBS Lett 581(16);3127-30. PMID: 17568582

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

Takagi64: Takagi Y, Sawada H (1964). "The metabolism of L-rhamnose in Escherichia coli. II. L-rhamnulose kinase." Biochim Biophys Acta 92;18-25. PMID: 14243778

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.

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

Wilson57: Wilson DM, Ajl S (1957). "Metabolism of L-rhamnose by Escherichia coli. II. The phosphorylation of L-rhamnulose." J Bacteriol 73(3);415-20. PMID: 13416205

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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