Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
BioCyc websites down
12/28 - 12/31
for maintenance.
twitter

Escherichia coli K-12 substr. MG1655 Protein: ribonuclease E inhibitor protein B



Gene: rraB Accession Numbers: G7885 (EcoCyc), b4255, ECK4248

Synonyms: yjgD

Regulation Summary Diagram: ?

Subunit composition of ribonuclease E inhibitor protein B = [RraB]2
         ribonuclease E inhibitor protein B = RraB

Summary:
RraB binds to the C-terminal half (CTH) of RNase E and interferes with the cleavage of a subset of RNase E target transcripts in vitro and in vivo. RraB interacts with RNase E at a distinct epitope within the CTH, while high-affinity binding of RraA, a second modulator of RNase E function, requires the CTH, but can not be mapped to a single epitope. Binding of RraA or RraB differently affect the composition of the degradosome [Gao06].

The regulatory interaction between RraB and RNase E and their orthologs appears to be evolutionarily conserved [Yeom08, Yeom08a]. RraB has been crystallized [Shen13a].

rraB is constitutively expressed [Zhou09].

RraB: "regulator of ribonuclease activity B" [Gao06]

Reviews: [Regnier09, Kaberdin09]

Citations: [Zou08]

Locations: cytosol

Map Position: [4,476,496 -> 4,476,912] (96.48 centisomes)
Length: 417 bp / 138 aa

Molecular Weight of Polypeptide: 15.603 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013936 , DIP:DIP-47905N , EchoBASE:EB2347 , EcoGene:EG12453 , EcoliWiki:b4255 , Mint:MINT-1243800 , ModBase:P0AF90 , OU-Microarray:b4255 , PortEco:rraB , Pride:P0AF90 , Protein Model Portal:P0AF90 , RefSeq:NP_418676 , RegulonDB:G7885 , SMR:P0AF90 , String:511145.b4255 , Swiss-Model:P0AF90 , UniProt:P0AF90

Relationship Links: InterPro:IN-FAMILY:IPR009671 , InterPro:IN-FAMILY:IPR016716 , Pfam:IN-FAMILY:PF06877

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006402 - mRNA catabolic process Inferred from experiment [Gao06]
GO:0043086 - negative regulation of catalytic activity Inferred from experiment [Gao06]
GO:0050790 - regulation of catalytic activity Inferred from experiment [Gao06]
GO:0060699 - regulation of endoribonuclease activity Inferred from experiment [Gao06]
GO:0060702 - negative regulation of endoribonuclease activity Inferred from experiment [Gao06]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0008428 - ribonuclease inhibitor activity Inferred from experiment [Gao06]
GO:0019899 - enzyme binding Inferred from experiment [Gao06]
GO:0042803 - protein homodimerization activity Inferred from experiment [Shen13a]
GO:0060698 - endoribonuclease inhibitor activity Inferred from experiment [Gao06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11a, UniProtGOA11]

MultiFun Terms: information transfer RNA related RNA degradation
regulation type of regulation posttranscriptional

Essentiality data for rraB 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:
Created 11-Nov-2013 by Keseler I , SRI International
Last-Curated ? 11-Nov-2013 by Keseler I , SRI International


Sequence Features

Feature Class Location Citations Comment
Protein-Segment 116 -> 134
[UniProt09]
UniProt: Asp/Glu-rich (acidic); Sequence Annotation Type: compositionally biased region;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
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

Butland05: Butland G, Peregrin-Alvarez JM, Li J, Yang W, Yang X, Canadien V, Starostine A, Richards D, Beattie B, Krogan N, Davey M, Parkinson J, Greenblatt J, Emili A (2005). "Interaction network containing conserved and essential protein complexes in Escherichia coli." Nature 433(7025);531-7. PMID: 15690043

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

Gao06: Gao J, Lee K, Zhao M, Qiu J, Zhan X, Saxena A, Moore CJ, Cohen SN, Georgiou G (2006). "Differential modulation of E. coli mRNA abundance by inhibitory proteins that alter the composition of the degradosome." Mol Microbiol 61(2);394-406. PMID: 16771842

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

Kaberdin09: Kaberdin VR, Lin-Chao S (2009). "Unraveling new roles for minor components of the E. coli RNA degradosome." RNA Biol 6(4);402-5. PMID: 19667755

Rajagopala14: Rajagopala SV, Sikorski P, Kumar A, Mosca R, Vlasblom J, Arnold R, Franca-Koh J, Pakala SB, Phanse S, Ceol A, Hauser R, Siszler G, Wuchty S, Emili A, Babu M, Aloy P, Pieper R, Uetz P (2014). "The binary protein-protein interaction landscape of Escherichia coli." Nat Biotechnol 32(3);285-90. PMID: 24561554

Regnier09: Regnier P, Hajnsdorf E (2009). "Poly(A)-assisted RNA decay and modulators of RNA stability." Prog Mol Biol Transl Sci 85;137-85. PMID: 19215772

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

Shen13a: Shen H, Liu H, Wang H, Teng M, Li X (2013). "Preliminary crystallographic analysis of RraB from Escherichia coli." Acta Crystallogr Sect F Struct Biol Cryst Commun 69(Pt 11);1268-71. PMID: 24192366

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

Yeom08: Yeom JH, Go H, Shin E, Kim HL, Han SH, Moore CJ, Bae J, Lee K (2008). "Inhibitory effects of RraA and RraB on RNAse E-related enzymes imply conserved functions in the regulated enzymatic cleavage of RNA." FEMS Microbiol Lett 285(1);10-5. PMID: 18510556

Yeom08a: Yeom JH, Shin E, Go H, Sim SH, Seong MJ, Lee K (2008). "Functional implications of the conserved action of regulators of ribonuclease activity." J Microbiol Biotechnol 18(8);1353-6. PMID: 18756093

Zhou09: Zhou L, Zhao M, Wolf RZ, Graham DE, Georgiou G (2009). "Transcriptional regulation of the Escherichia coli gene rraB, encoding a protein inhibitor of RNase E." J Bacteriol 191(21);6665-74. PMID: 19717586

Zou08: Zou Z, Cao L, Zhou P, Su Y, Sun Y, Li W (2008). "Hyper-acidic protein fusion partners improve solubility and assist correct folding of recombinant proteins expressed in Escherichia coli." J Biotechnol 135(4);333-9. PMID: 18599143

Other References Related to Gene Regulation

Khodursky00a: Khodursky AB, Peter BJ, Cozzarelli NR, Botstein D, Brown PO, Yanofsky C (2000). "DNA microarray analysis of gene expression in response to physiological and genetic changes that affect tryptophan metabolism in Escherichia coli." Proc Natl Acad Sci U S A 97(22);12170-5. PMID: 11027315

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 Mon Dec 22, 2014, biocyc13.