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Escherichia coli K-12 substr. MG1655 Protein: predicted enamine/imine deaminase



Gene: ridA Accession Numbers: G7877 (EcoCyc), b4243, ECK4238

Synonyms: yjgF

Regulation Summary Diagram: ?

Subunit composition of predicted enamine/imine deaminase = [RidA]3
         predicted enamine/imine deaminase = RidA

Summary:
Experimental work in Salmonella enterica serovar Typhimurium has identified an enamime/imine deaminase activity as the biochemical function of the conserved YjgF protein family [Lambrecht12]. A ridA mutation causes pleiotropic metabolic phenotypes [EnosBerlage98].

A crystal structure of E. coli RidA has been solved at 1.2 Å resolution. RidA is homotrimeric and exhibits some structural similarity to protein tyrosine phosphatases and to Bacillus subtilis chorismate mutase. However, RidA was not expected to share these enzymatic activities [Volz99].

RidA can be modified with fatty acid metabolites in vitro; based on the analysis of a C107S mutant, the modification may occur at C107 [Rangan10].

RidA: "reactive intermediate/imine deaminase A" [Lambrecht12]

Citations: [Irving01]

Locations: cytosol, membrane

Map Position: [4,468,550 <- 4,468,936] (96.31 centisomes)
Length: 387 bp / 128 aa

Molecular Weight of Polypeptide: 13.612 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013886 , DIP:DIP-36232N , EchoBASE:EB2415 , EcoGene:EG12524 , EcoliWiki:b4243 , ModBase:P0AF93 , OU-Microarray:b4243 , PortEco:yjgF , Pride:P0AF93 , Protein Model Portal:P0AF93 , RefSeq:NP_418664 , RegulonDB:G7877 , SMR:P0AF93 , String:511145.b4243 , Swiss-Model:P0AF93 , UniProt:P0AF93

Relationship Links: InterPro:IN-FAMILY:IPR006056 , InterPro:IN-FAMILY:IPR006175 , InterPro:IN-FAMILY:IPR013813 , InterPro:IN-FAMILY:IPR019897 , Panther:IN-FAMILY:PTHR11803 , PDB:Structure:1QU9 , Pfam:IN-FAMILY:PF01042 , Prosite:IN-FAMILY:PS01094

In Paralogous Gene Group: 494 (4 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0008652 - cellular amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0009082 - branched-chain amino acid biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0009097 - isoleucine biosynthetic process Inferred by computational analysis [UniProtGOA11]
GO:0009636 - response to toxic substance Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
GO:0019239 - deaminase activity Inferred by computational analysis [GOA01, GOA, Lambrecht12]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: cell processes adaptations other (mechanical, nutritional, oxidative stress)
metabolism

Essentiality data for ridA knockouts: ?

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

Credits:
Last-Curated ? 22-Nov-2011 by Keseler I , SRI International


Sequence Features

Feature Class Location Common Name Citations Comment
Cleavage-of-Initial-Methionine 1  
[Frutiger96, Link97, UniProt11, Wasinger98]
UniProt: Removed.
Chain 2 -> 128  
[UniProt09]
UniProt: UPF0076 protein yjgF;
Amino-Acid-Site 17  
[UniProt12]
UniProt: Stabilizes the substrate; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.
Amino-Acid-Sites-That-Bind 105  
[UniProt12]
UniProt: Substrate; Non-Experimental Qualifier: potential.
Modified-Residue 107 possible lipid modification site
[Rangan10]
 
Amino-Acid-Site 120  
[UniProt12]
UniProt: Role at high pH; Sequence Annotation Type: site; Non-Experimental Qualifier: by similarity.


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
Peter D. Karp on Wed Jan 18, 2006:
Gene right-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
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

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

EnosBerlage98: Enos-Berlage JL, Langendorf MJ, Downs DM (1998). "Complex metabolic phenotypes caused by a mutation in yjgF, encoding a member of the highly conserved YER057c/YjgF family of proteins." J Bacteriol 180(24);6519-28. PMID: 9851994

Frutiger96: Frutiger S., Hughes G.J., Pasquali C., Hochstrasser D.F. (1996). Data submission to UniProtKB on 1996-02.

GOA: GOA "Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity."

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Irving01: Irving JA, Whisstock JC, Lesk AM (2001). "Protein structural alignments and functional genomics." Proteins 42(3);378-82. PMID: 11151008

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Lambrecht12: Lambrecht JA, Flynn JM, Downs DM (2012). "Conserved YjgF protein family deaminates reactive enamine/imine intermediates of pyridoxal 5'-phosphate (PLP)-dependent enzyme reactions." J Biol Chem 287(5);3454-61. PMID: 22094463

Lasserre06: Lasserre JP, Beyne E, Pyndiah S, Lapaillerie D, Claverol S, Bonneu M (2006). "A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis." Electrophoresis 27(16);3306-21. PMID: 16858726

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Rangan10: Rangan KJ, Yang YY, Charron G, Hang HC (2010). "Rapid visualization and large-scale profiling of bacterial lipoproteins with chemical reporters." J Am Chem Soc 132(31);10628-9. PMID: 20230003

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

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

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

UniProt12: UniProt Consortium (2012). "UniProt version 2012-09 released on 2012-09-12 00:00:00." Database.

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

Volz99: Volz K (1999). "A test case for structure-based functional assignment: the 1.2 A crystal structure of the yjgF gene product from Escherichia coli." Protein Sci 8(11);2428-37. PMID: 10595546

Wasinger98: Wasinger VC, Humphery-Smith I (1998). "Small genes/gene-products in Escherichia coli K-12." FEMS Microbiol Lett 169(2);375-82. PMID: 9868784

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305


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 Dec 19, 2014, biocyc13.