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Escherichia coli K-12 substr. MG1655 Protein: enamine/imine deaminase, redox regulated chaperone

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

Synonyms: yjgF

Regulation Summary Diagram

Regulation summary diagram for ridA

Subunit composition of enamine/imine deaminase, redox regulated chaperone = [RidA]3
         enamine/imine deaminase, redox regulated chaperone = RidA


In E. coli K-12 the conserved protein RidA has been characterised as a redox-regulated chaperone that is activated in response to hypochlorous acid (HOCl) stress. RidA activation is mediated by chlorination; RidA activation is accompanied by loss of free amino groups and increased hydrophobicity. Chlorination of RidA is reversible; N-chlorinated RidA is reduced by dithiothreitol and ascorbic acid in vitro and by glutathione and thioredoxin in vivo [Muller14].

Purified RidA is active as an enamine/imine deaminase in vitro [Lindemann13].

HOCl treated RidA and monochloramine (a HOCl derived chloramine) treated RidA both prevent aggregation of denatured citrate synthase in vitro [Muller14].

Deletion of ridA in an E. coli BL21 strain results in increased sensitivity to HOCl; lack of ridA may be lethal in E. coli K-12 MC4100 [Muller14].

Purified, crystallised RidA is homotrimeric; the structure contains a covalent modification on the Sγ of Cys107 [Volz99]. RidA is oxidised at Cys107 by peroxynitrite treatment; purified RidA accelerates the IlvA dependent formation of 2-ketobutyrate from threonine in vitro; when treated with peroxynitrite this effect is eliminated; a RidA(C107S) substitution mutant retains the activating effect but can no longer be inactivated by peroxynitrite treatment [Lindemann13].

A RidA(C107S) substitution mutant retains chaperone activity after HOCl treatment [Muller14].

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, 347°)
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

Gene-Reaction Schematic

GO Terms:
Biological Process:
Inferred from experimentInferred by computational analysisGO:0009636 - response to toxic substance [UniProtGOA11a, Muller14]
Inferred by computational analysisGO:0008652 - cellular amino acid biosynthetic process [UniProtGOA11a]
Inferred by computational analysisGO:0009082 - branched-chain amino acid biosynthetic process [UniProtGOA11a]
Inferred by computational analysisGO:0009097 - isoleucine biosynthetic process [UniProtGOA11a]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0019239 - deaminase activity [GOA01a, Lindemann13, GOA, Lambrecht12]
Inferred from experimentGO:0042802 - identical protein binding [Volz99]
Inferred from experimentGO:0051082 - unfolded protein binding [Muller14]
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0005829 - cytosol [DiazMejia09, Ishihama08, LopezCampistrou05]
Inferred from experimentGO:0016020 - membrane [Lasserre06]
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a]

MultiFun Terms: cell processesadaptationsother (mechanical, nutritional, oxidative stress)

Essentiality data for ridA knockouts:

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

Curated 22-Nov-2011 by Keseler I, SRI International
Last-Curated 18-Jan-2015 by Mackie A, Macquarie University

Sequence Features

Protein sequence of enamine/imine deaminase, redox regulated chaperone with features indicated

Feature Class Location Common Name Citations Comment
Cleavage-of-Initial-Methionine 1  
Inferred from experimentAuthor statement[Link97, Frutiger96, Link97, UniProt11, Wasinger98]
UniProt: Removed.
Chain 2 -> 128  
Author statement[UniProt15]
UniProt: 2-iminobutanoate/2-iminopropanoate deaminase.
Pfam PF01042 7 -> 126  
Inferred by computational analysis[Finn14]
Ribonuc_L-PSP : Endoribonuclease L-PSP
Amino-Acid-Site 17  
Inferred by computational analysis[UniProt15]
UniProt: Stabilizes the substrate; Sequence Annotation Type: site.
Amino-Acid-Sites-That-Bind 105  
Inferred by computational analysis[UniProt15]
UniProt: Substrate.
Modified-Residue 107 possible lipid modification site
Inferred from experiment[Rangan10]
Amino-Acid-Site 120  
Inferred by computational analysis[UniProt15]
UniProt: Important for catalytic activity at high pH; Sequence Annotation Type: site.

Gene Local Context (not to scale -- see Genome Browser for correct scale)

Gene local context diagram

Transcription Unit

Transcription-unit diagram


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.


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

Finn14: Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, Heger A, Hetherington K, Holm L, Mistry J, Sonnhammer EL, Tate J, Punta M (2014). "Pfam: the protein families database." Nucleic Acids Res 42(Database issue);D222-30. PMID: 24288371

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."

GOA01a: 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

Lindemann13: Lindemann C, Lupilova N, Muller A, Warscheid B, Meyer HE, Kuhlmann K, Eisenacher M, Leichert LI (2013). "Redox proteomics uncovers peroxynitrite-sensitive proteins that help Escherichia coli to overcome nitrosative stress." J Biol Chem 288(27);19698-714. PMID: 23696645

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

Muller14: Muller A, Langklotz S, Lupilova N, Kuhlmann K, Bandow JE, Leichert LI (2014). "Activation of RidA chaperone function by N-chlorination." Nat Commun 5;5804. PMID: 25517874

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

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-08 released on 2015-07-22." Database.

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

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords 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

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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