Escherichia coli K-12 substr. MG1655 Enzyme: L-rhamnonate dehydratase

Gene: yfaW Accession Numbers: G7160 (EcoCyc), b2247, ECK2240

Regulation Summary Diagram: ?

Regulation summary diagram for yfaW

Subunit composition of L-rhamnonate dehydratase = [YfaW]8
         L-rhamnonate dehydratase = YfaW

YfaW is a L-rhamnonate dehydratase (RhamD) with promiscuous substrate specificity [Rakus08].

RhamD is a member of the mandelate racemase (MR) subgroup of the enolase superfamily. A crystal structure has been solved at 2.1 Å resolution, where the enzyme is a tetramer of dimers. Although the enzyme is also an octamer in solution, based on the location of the active site, the minimum functional unit appears to be the monomer. A reaction mechanism and likely catalytic residues have been proposed, and site-directed mutants were assayed to confirm lack of activity [Rakus08].

Locations: cytosol

Map Position: [2,358,231 <- 2,359,448] (50.83 centisomes, 183°)
Length: 1218 bp / 405 aa

Molecular Weight of Polypeptide: 44.714 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007436 , DIP:DIP-11955N , EchoBASE:EB3838 , EcoGene:EG14085 , EcoliWiki:b2247 , ModBase:P77215 , OU-Microarray:b2247 , PortEco:yfaW , Protein Model Portal:P77215 , RefSeq:NP_416750 , RegulonDB:G7160 , SMR:P77215 , String:511145.b2247 , UniProt:P77215

Relationship Links: InterPro:IN-FAMILY:IPR001354 , InterPro:IN-FAMILY:IPR013341 , InterPro:IN-FAMILY:IPR013342 , InterPro:IN-FAMILY:IPR018110 , InterPro:IN-FAMILY:IPR023444 , InterPro:IN-FAMILY:IPR029017 , InterPro:IN-FAMILY:IPR029065 , Panther:IN-FAMILY:PTHR13794 , PDB:Structure:2I5Q , Pfam:IN-FAMILY:PF01188 , Pfam:IN-FAMILY:PF02746 , Prosite:IN-FAMILY:PS00908 , Smart:IN-FAMILY:SM00922

In Paralogous Gene Group: 394 (4 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0008152 - metabolic process Inferred by computational analysis [GOA01a]
GO:0009063 - cellular amino acid catabolic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0050032 - L-rhamnonate dehydratase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Rakus08]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01a]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Essentiality data for yfaW knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Created 05-Sep-2008 by Keseler I , SRI International
Last-Curated ? 05-Sep-2008 by Keseler I , SRI International

Enzymatic reaction of: L-rhamnonate dehydratase

Synonyms: RhamD

EC Number:

L-rhamnonate <=> 2-dehydro-3-deoxy-L-rhamnonate + H2O

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

Reversibility of this reaction is unspecified.

Alternative Substrates for L-rhamnonate: L-lyxonate [Rakus08 ] , L-mannonate [Rakus08 ]

Cofactors or Prosthetic Groups: Mg2+ [Rakus08]

Kinetic Parameters:

Km (μM)

Sequence Features

Protein sequence of L-rhamnonate dehydratase with features indicated

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 29
UniProt: Substrate.
Mutagenesis-Variant 29
[Rakus08, UniProt11]
UniProt: Loss of activity due to absence of substrate binding.
Amino-Acid-Sites-That-Bind 55
UniProt: Substrate; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 222
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 248
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 276
UniProt: Magnesium; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 277
[Rakus08, UniProt11]
UniProt: 35-fold decrease in activity. 59- fold decrease in substrate affinity.
Amino-Acid-Site 298
UniProt: Increases basicity of active site His; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity;
Active-Site 325
UniProt: Proton acceptor.
Mutagenesis-Variant 325
[Rakus08, UniProt11]
UniProt: Loss of activity. 2-fold decrease in substrate affinity.
Amino-Acid-Sites-That-Bind 345
UniProt: Substrate; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Units:

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram


Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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."

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Rakus08: Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA (2008). "Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase." Biochemistry 47(38);9944-54. PMID: 18754693

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 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."

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 19.0 on Fri Oct 9, 2015, biocyc12.