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Escherichia coli K-12 substr. MG1655 Enzyme: L-galactonate oxidoreductase



Gene: lgoD Accession Numbers: G7945 (EcoCyc), b4358, ECK4348

Synonyms: yjjN

Regulation Summary Diagram: ?

Summary:
YjjN is an L-galactonate oxidoreductase [Kuivanen14] that is required for growth on L-galactonate as the sole carbon source under high-throughput growth conditions with limited aeration [Reed06]. YjjN did not show dehydrogenase activity in a high-throughput screen of purified proteins; however, L-galactonate was not tested as a substrate [Kuznetsova05]. YjjN may be the L-galactonate oxidoreductase involved in the degradation of L-galactonate that was described in [Cooper79].

Expression of yjjN is increased during growth on L-galactonate compared to growth on L-lactate [Reed06]. UxuR appears to regulate yjjN expression [Suvorova11].

Locations: cytosol

Map Position: [4,594,013 -> 4,595,035] (99.02 centisomes)
Length: 1023 bp / 340 aa

Molecular Weight of Polypeptide: 36.448 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0014294 , EchoBASE:EB2475 , EcoGene:EG12590 , EcoliWiki:b4358 , ModBase:P39400 , OU-Microarray:b4358 , PortEco:yjjN , Protein Model Portal:P39400 , RefSeq:NP_418778 , RegulonDB:G7945 , SMR:P39400 , String:511145.b4358 , UniProt:P39400

Relationship Links: InterPro:IN-FAMILY:IPR002085 , InterPro:IN-FAMILY:IPR002328 , InterPro:IN-FAMILY:IPR011032 , InterPro:IN-FAMILY:IPR013149 , InterPro:IN-FAMILY:IPR013154 , InterPro:IN-FAMILY:IPR016040 , Panther:IN-FAMILY:PTHR11695 , Pfam:IN-FAMILY:PF00107 , Pfam:IN-FAMILY:PF08240 , Prosite:IN-FAMILY:PS00059

In Paralogous Gene Group: 103 (13 members)

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

GO Terms:

Biological Process: GO:0034195 - L-galactonate catabolic process Inferred from experiment [Reed06]
GO:0055114 - oxidation-reduction process Inferred by computational analysis [UniProtGOA11, GOA01]
Molecular Function: GO:0016616 - oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor Inferred by computational analysis Inferred from experiment [Kuivanen14, Reed06]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA01]
GO:0016491 - oxidoreductase activity Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: metabolism carbon utilization carbon compounds

Essentiality data for lgoD 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]
Yes [Feist07, Comment 4]

Credits:
Last-Curated ? 09-Jun-2014 by Keseler I , SRI International


Enzymatic reaction of: L-galactonate oxidoreductase

aldehydo-L-galactonate + NAD+ <=> D-tagaturonate + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is favored in the direction shown.

Alternative Substrates for aldehydo-L-galactonate: L-gulonate [Kuivanen14 ]

In Pathways: L-galactonate degradation

Summary:
The reaction equilibrium is predicted to be 0.019 at pH 8, i.e. favoring the reduction of D-tagaturonate [Kuivanen14].

Cofactors or Prosthetic Groups: Zn2+ [Kuivanen14]

Kinetic Parameters:

Substrate
Km (μM)
kcat (sec-1)
kcat/Km (sec-1 μM-1)
Citations
aldehydo-L-galactonate
19500.0
0.51
[Kuivanen14]

pH(opt): 8.0 [Kuivanen14]


Sequence Features

Feature Class Location Citations Comment
Metal-Binding-Site 40
[UniProt10]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 65
[UniProt10]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 92
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 95
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 98
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 106
[UniProt10]
UniProt: Zinc 2; Non-Experimental Qualifier: by similarity;
Metal-Binding-Site 146
[UniProt10]
UniProt: Zinc 1; catalytic; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Cooper79: Cooper RA (1979). "The pathway for L-galactonate catabolism in Escherichia coli K-12." FEBS Lett 103(2);216-20. PMID: 381020

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

Feist07: Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO (2007). "A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information." Mol Syst Biol 3;121. PMID: 17593909

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."

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

Kuivanen14: Kuivanen J, Richard P (2014). "The yjjN of E. coli codes for an L-galactonate dehydrogenase and can be used for quantification of L-galactonate and L-gulonate." Appl Biochem Biotechnol. PMID: 24861318

Kuznetsova05: Kuznetsova E, Proudfoot M, Sanders SA, Reinking J, Savchenko A, Arrowsmith CH, Edwards AM, Yakunin AF (2005). "Enzyme genomics: Application of general enzymatic screens to discover new enzymes." FEMS Microbiol Rev 29(2);263-79. PMID: 15808744

Reed06: Reed JL, Patel TR, Chen KH, Joyce AR, Applebee MK, Herring CD, Bui OT, Knight EM, Fong SS, Palsson BO (2006). "Systems approach to refining genome annotation." Proc Natl Acad Sci U S A 103(46);17480-4. PMID: 17088549

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

Suvorova11: Suvorova IA, Tutukina MN, Ravcheev DA, Rodionov DA, Ozoline ON, Gelfand MS (2011). "Comparative genomic analysis of the hexuronate metabolism genes and their regulation in gammaproteobacteria." J Bacteriol 193(15);3956-63. PMID: 21622752

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProtGOA11: 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 18.5 on Thu Dec 18, 2014, BIOCYC14B.