Escherichia coli K-12 substr. MG1655 Enzyme: 2-keto-3-deoxy-L-rhamnonate aldolase

Gene: yfaU Accession Numbers: G7158 (EcoCyc), b2245, ECK2238

Regulation Summary Diagram: ?

Regulation summary diagram for yfaU

Subunit composition of 2-keto-3-deoxy-L-rhamnonate aldolase = [YfaU]6
         2-keto-3-deoxy-L-rhamnonate aldolase = YfaU

YfaU is a 2-keto-3-deoxy-L-rhamnonate aldolase which catalyzes a retro-aldol reaction with somewhat relaxed substrate specificity [Rea08, Rakus08].

Crystal structures of the enzyme alone and in a product complex with Mg2+-pyruvate have been solved, showing a trimer of domain-swapped dimers with (β/α)8 barrel subunits typical of the divalent metal ion-dependent class II aldolases. The architecture of the active site and a predicted catalytic mechanism are discussed. Site-directed mutagenesis confirmed the importance of Arg74 and His49 for catalysis [Rea08].

Citations: [Wright02]

Locations: cytosol

Map Position: [2,356,064 <- 2,356,867] (50.78 centisomes, 183°)
Length: 804 bp / 267 aa

Molecular Weight of Polypeptide: 28.916 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007431 , DIP:DIP-11953N , EchoBASE:EB3836 , EcoGene:EG14083 , EcoliWiki:b2245 , ModBase:P76469 , OU-Microarray:b2245 , PortEco:yfaU , Protein Model Portal:P76469 , RefSeq:NP_416748 , RegulonDB:G7158 , SMR:P76469 , String:511145.b2245 , Swiss-Model:P76469 , UniProt:P76469

Relationship Links: InterPro:IN-FAMILY:IPR005000 , InterPro:IN-FAMILY:IPR015813 , InterPro:IN-FAMILY:IPR023593 , PDB:Structure:2VWS , PDB:Structure:2VWT , Pfam:IN-FAMILY:PF03328

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0005975 - carbohydrate metabolic process Inferred by computational analysis [Gaudet10]
GO:0006725 - cellular aromatic compound metabolic process Inferred by computational analysis [Rea08]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rea08]
GO:0016151 - nickel cation binding Inferred from experiment [Rea08]
GO:0016832 - aldehyde-lyase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Rea08]
GO:0000287 - magnesium ion binding Inferred by computational analysis [GOA06]
GO:0003824 - catalytic activity Inferred by computational analysis [GOA01]
GO:0016829 - lyase activity Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Rea08]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Essentiality data for yfaU 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 08-Sep-2008 by Keseler I , SRI International
Last-Curated ? 08-Sep-2008 by Keseler I , SRI International

Enzymatic reaction of: 2-keto-3-deoxy-L-rhamnonate aldolase

EC Number:

2-dehydro-3-deoxy-L-rhamnonate <=> pyruvate + (S)-lactaldehyde

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 2-dehydro-3-deoxy-L-rhamnonate: 2-dehydro-3-deoxy-L-mannonate [Rea08 , Rakus08 ]

Although Ni2+ is unlikely to be the physiologically relevant metal cofactor, the enzyme shows higher turnover with Ni2+ present than with Mg2+ [Rea08].

Cofactors or Prosthetic Groups: Mg2+ [Rea08]

Kinetic Parameters:

Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
[Rea08, BRENDA14]
0.3, 0.4
0.0038, 0.0051
[Rakus08, BRENDA14]

Sequence Features

Protein sequence of 2-keto-3-deoxy-L-rhamnonate aldolase with features indicated

Feature Class Location Citations Comment
Active-Site 49
UniProt: Proton acceptor.
Mutagenesis-Variant 49
[Rea08, UniProt11]
UniProt: Loss of activity.
Amino-Acid-Site 74
UniProt: Transition state stabilizer; Sequence Annotation Type: site.
Mutagenesis-Variant 74
[Rea08, UniProt11]
UniProt: Loss of activity.
Amino-Acid-Site 88
UniProt: Increases basicity of active site His; Sequence Annotation Type: site.
Amino-Acid-Sites-That-Bind 151
UniProt: Substrate.
Metal-Binding-Site 153
[Rea08, UniProt15]
UniProt: Magnesium.
Amino-Acid-Sites-That-Bind 178
UniProt: Substrate; via amide nitrogen.
Metal-Binding-Site 179
[Rea08, UniProt15]
UniProt: Magnesium.

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

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

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

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

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, 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

Rea08: Rea D, Hovington R, Rakus JF, Gerlt JA, Fulop V, Bugg TD, Roper DI (2008). "Crystal structure and functional assignment of YfaU, a metal ion dependent class II aldolase from Escherichia coli K12." Biochemistry 47(38);9955-65. PMID: 18754683

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.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wright02: Wright A, Blewett A, Fulop V, Cooper R, Burrows S, Jones C, Roper D (2002). "Expression, purification, crystallization and preliminary characterization of an HHED aldolase homologue from Escherichia coli K12." Acta Crystallogr D Biol Crystallogr 58(Pt 12);2191-3. PMID: 12454498

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 Tue Oct 6, 2015, biocyc13.