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-rhamnulose kinase



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

Regulation Summary Diagram: ?

Summary:
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)
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: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0019301 - rhamnose catabolic process Inferred from experiment Inferred by computational analysis [UniProtGOA12, GOA01a, Power67]
GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [GOA01a]
GO:0016310 - phosphorylation Inferred by computational analysis [UniProtGOA11a]
GO:0019299 - rhamnose metabolic process Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0046835 - carbohydrate phosphorylation Inferred by computational analysis [GOA06, GOA01, GOA01a]
Molecular Function: GO:0008993 - rhamnulokinase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Fessner92]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a]
GO:0005524 - ATP 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:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Credits:
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: 2.7.1.5

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

Summary:
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:

Substrate
Km (μM)
Citations
L-rhamnulofuranose
82.0
[Chiu64]
ATP
110.0
[Chiu64]

pH(opt): 8.5 [Chiu64]


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 14
[UniProt10]
UniProt: ATP;
Sequence-Conflict 214
[Moralejo93, UniProt10]
Alternate sequence: G → missing; UniProt: (in Ref. 1; CAA43001);
Protein-Segment 236 -> 238
[UniProt10a]
UniProt: Substrate binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 259
[UniProt10]
UniProt: ATP;
Amino-Acid-Sites-That-Bind 296
[UniProt10]
UniProt: Substrate;
Amino-Acid-Sites-That-Bind 304
[UniProt10]
UniProt: ATP;
Sequence-Conflict 388 -> 389
[Moralejo93, UniProt10]
Alternate sequence: QL → HV; UniProt: (in Ref. 1; CAA43001);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3904 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11868; confirmed by SwissProt match.


References

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.

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.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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


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 Fri Nov 28, 2014, biocyc12.