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MetaCyc Enzyme: 2-keto-3-deoxy-L-rhamnonate aldolase

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

Species: Escherichia coli K-12 substr. MG1655

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

Summary:
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]

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: ?

GO Terms:

Biological Process: 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, GOA01a, Rea08]
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:0005737 - cytoplasm Inferred from experiment [Rea08]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism

Credits:
Created in EcoCyc 08-Sep-2008 by Keseler I , SRI International
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International


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

EC Number: 4.1.2.53

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.

This reaction is reversible.

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

Credits:
Imported from EcoCyc 16-Sep-2014 by Paley S , SRI International

Summary:
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:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
2-dehydro-3-deoxy-L-rhamnonate
78.0
[Rea08, BRENDA14]
2-dehydro-3-deoxy-L-rhamnonate
78.0
0.3, 0.4
[Rakus08, BRENDA14]


Sequence Features

Feature Class Location Citations Comment
Mutagenesis-Variant 49
[Rea08, UniProt11]
Alternate sequence: A; UniProt: Loss of activity.
Active-Site 49
[UniProt10a]
UniProt: Proton acceptor;
Mutagenesis-Variant 74
[Rea08, UniProt11]
Alternate sequence: A; UniProt: Loss of activity.
Amino-Acid-Site 74
[UniProt10a]
UniProt: Transition state stabilizer; Sequence Annotation Type: site;
Amino-Acid-Site 88
[UniProt10a]
UniProt: Increases basicity of active site His; Sequence Annotation Type: site;
Amino-Acid-Sites-That-Bind 151
[UniProt10a]
UniProt: Substrate;
Metal-Binding-Site 153
[UniProt10a]
UniProt: Magnesium;
Amino-Acid-Sites-That-Bind 178
[UniProt10a]
UniProt: Substrate; via amide nitrogen;
Metal-Binding-Site 179
[UniProt10a]
UniProt: Magnesium;

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


References

BRENDA14: BRENDA team (2014). "Imported from BRENDA version existing on Aug 2014." http://www.brenda-enzymes.org.

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

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."

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProtGOA11a: 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 MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Sat Nov 22, 2014, biocyc14.