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MetaCyc Enzyme: ribonuclease E

Gene: rne Accession Numbers: EG10859 (MetaCyc), b1084, ECK1069

Synonyms: smbB, ams, hmp1, RNase E

Species: Escherichia coli K-12 substr. MG1655

Component of: degradosome (extended summary available)

Subunit composition of ribonuclease E = [Rne]4
         RNase E = Rne

Summary:
Ribonuclease E (RNase E) is a single-strand-specific endonuclease that is essential for viability. It processes rRNA, tRNA and other RNAs, is involved in plasmid and phage stability and is part of the degradosome, a multienzyme complex involved in mRNA degradation.

RNase E is involved in processing and cleavage of several rRNAs. It processes the 9S rRNA precursor to yield the mature 5S rRNA by cleaving quite near the 5' end and downstream from the 3' end of the final product [Ghora78, Roy83, Apirion78]. RNase E also participates in the 5' maturation of 16S rRNA from its 17S precursor, as well as being able to cleave single-stranded regions within mature 16S and 23S rRNAs [Li99b, Bessarab98].

RNase E initiates the processing of both poly- and monicistronic tRNA transcripts, including those within rRNA transcripts, by cleaving within a few nucleotides of the mature 3' CCA terminus, thus allowing RNase P and other 3' to 5' exonucleases to complete tRNA maturation [Ow02, Li02]. RNase E similarly cleaves at the 3' CCA terminus of the ssrA RNA precursor to yield its final form [LinChao99]. RNase E may also be involved in processing of the 5' leader of precursor tRNAs [Soderbom05].

RNase E carries out the 3' processing of M1 mRNA, which codes for the catalytic subunit of RNase P [Lundberg95, Sim01]. Other mRNA processing substrates include the cell division inhibitor DicF, the RNA polymerase sigma70 activity modulator 6S RNA, the polycistronic histidine operon mRNA and the papAB primary transcript, which is cleaved to yield stable papA and unstable papB mRNA [Faubladier90, Kim04, Alifano94, Nilsson91]. Domains of RNase E have been identified that are important for the degradation of the Rep mRNA of the ColE2 plasmid, versus the antisense RNA that controls its expression [Nishio09].

The stability of plasmids R1 and Colicin E1 is influenced by RNase E. It initiates degradation of CopA, the R1 copy regulator RNA [Soderbom98]. RNase E also cleaves near the 5' end of the sok component of the hok/sok sense/antisense RNA plasmid stabilization mechanism from R1, allowing subsequent degradation by another degradosome component, PNPase [Dam97]. The Colicin E1 DNA synthesis inhibitor RNA, RNAI, is also cleaved at its 5' end by RNase E [Tomcsanyi85, LinChao91]. Finally, RNase E cleaves FinP, which binds to the 5'-untranslated region of the positive F-plasmid transfer regulator traJ [Jerome99].

RNase E processing maintains the balance between phage f1 proteins pII and PX by cleaving the mRNA coding for pII, thus maintaining a normal replication cycle [Kokoska98]. RNase E is required more generally for production of certain phage f1 mRNAs as well [Stump96]. RNase E processes T4 gene 32 mRNA, cleaves T4 soc mRNA and is involved generally in the destabilizing of T4 mRNA [Mudd88, Otsuka03, Mudd90]. Conversely, the T4 Srd protein stimulates RNase E to degrade host mRNAs [Qi15].

A number of cellular mRNAs are degraded by RNase E. mRNA decay slows 2-3 fold in an rne mutant, and RNase E is the rate-limiting enzyme in the degradation of many of its substrates [Babitzke91, Jain02]. RNase E cleaves both sodB mRNA and its antisense RNA RyhB, though cleavage of the latter can be blocked by Hfq binding to the cleavage site [Afonyushkin05, Masse03, Moll03a, Folichon03]. Hfq also overlaps cleavage sites in the dsrA and ompA mRNAs [Moll03a]. The rpsO-pnp transcript is cleaved near the beginning of the rpsO coding sequence and on both sides of the rpsO 3' stem-loop terminator, after which it is rapidly degraded by PNPase [Hajnsdorf99, Regnier91, Braun96, Hajnsdorf94]. Ribosome binding blocks this cleavage [Braun98]. RNase E is responsible for a number of cleavages within the unc transcripts, which code for subunits of the F1/F0-ATPase [Patel92, Patel95]. It destabilizes the secE, nusG, L11-L1, L10 and beta cistrons from transcripts from the secEnusG and rplKAJLrpoBC operons, though this is not reflected in a change in mRNA abundance [Chow94]. Other transcripts that are degraded by RNase E include ftsA-ftsZ, thrS, pstG, pnp and rnb [Cam96, Nogueira01, Kimata01, Hajnsdorf94a, Zilhao95, Tamura06]. RNase E is also involved in limiting the abundance of mRNAs from rspT, dsbC, pth and tetR [Le02, Zhan04, CruzVera02, Baumeister91]. Finally, although overexpressed RNase G can partially complement a lack of RNase E, about a hundred RNAs are only degraded by RNase E, including many mRNAs coding for proteins involved in energy generation and macromolecule synthesis and degradation [Lee02a].

RNase E regulates its own abundance by cleaving within the 5' untranslated region of rne mRNA. Autoregulation occurs via specific binding of the catalytic domain to the hp2 region of its transcript. As RNase E activity can be titrated by other substrates, this acts to modulate its expression to match cellular needs [Mudd93, Diwa02, Sousa01, Schuck09]. Appending the 5' region of rne to heterologous RNA confers RNase E regulation [Jain95].

In a pnp/rnb/rne triple mutant, RNA polyadenylation is longer and more abundant [OHara95]. Conversely, RNase E indirectly increases polyadenylation by generating new 3' ends on which PAP I, which has a binding region for RNase E, can act [Mohanty00, Raynal99]. Increased polyadenylation stabilizes the rne transcript [Mohanty99, Mohanty02].

RNase E cleaves at regions that are single stranded and rich in A/U sequences [Kim04b, Mackie92, Bessarab98, Babitzke91]. Though RNase E has no canonical target sequence, the effects of local sequence on cleavage placement and effectiveness have been thoroughly characterized [Kaberdin03, McDowall94]. Secondary structure in the form of adjacent stem-loops has been shown to be necessary for RNase E cleavage for a number of substrates, and it has been suggested that these structures maintain a stretch of single-stranded RNA for the enzyme to cleave [Ehretsmann92, Cormack92, Diwa00]. In other cases, however, secondary structures play no definite role in susceptibility or actually impede RNase E cleavage [Mackie93, McDowall95, Lopez96].

RNase E binds to the 5'-monophosphate end of its substrate but then cleaves farther in moving 3' to 5', suggesting a scanning mechanism [Feng02]. In the absence of a 5'-monophosphate, cleavage is slowed [Jiang04]. Blocking the 5' end, either by circularizing the RNA or by adding a 5'-triphosphate also inhibits cleavage [Mackie00, Mackie98]. However, evidence and requirements for a 5' end-independent mechanism of mRNA degradation by RNase E has also been presented [Kime10] and the mechanism of tRNA processing in the absence of recognition of a 5'-monophosphorylated end has been studied [Kime14]. Contrary to previous studies, RNA-seq analysis showed that the 5'-monophosphate-independent (direct entry) cleavage of RNA by RNase E appears to be a major RNA degradation pathway in E. coli [Clarke14].

The catalytic parameters of RNase E have been thoroughly evaluated [Redko03].

RNase E's enzymatic and RNA-binding functions are split between its amino-terminal and carboxy-terminal portions, respectively [McDowall96, Taraseviciene95]. The carboxy-terminal section of the protein and its arginine-rich RNA-binding domain (ARRBD) is required for mRNA degradation and enhances RNase E autoregulatory cleavage of rne mRNA, but is dispensable for rRNA processing [Ow00, Lopez99, Jiang00, Kaberdin00]. Contradicting this observation, it has been reported that the RNA-binding domain of RNase E is not required for feedback regulation [Diwa02a]. Mutations within the RNA-binding do lead to defective binding, but have no effect on RNA cleavage activity [Shin08].

RNase E is catalytically active only as a tetramer, with its RNA-binding domains facing outward [Callaghan03]. However, a conserved RNase E peptide lacking the tetramerization domain was shown to retain core catalytic function [Caruthers06]. Crystallographic and NMR analysis of the isolated RNA-binding domain indicates that it forms a homodimer, possibly contributing to overall tetramer formation [Schubert04]. A crystal structure of the amino-terminal catalytic domain to 2.9 Å resolution shows that the tetramer consists of a dimer of dimers and contains divalent magnesium ion [Callaghan05]. The tetrameric structure is maintained by cysteine-zinc-cysteine linkages between adjacent Rne monomers [Callaghan05a]. Additional crystal structures of the RNase E catalytic domain have been presented [Koslover08], as well as structures of a segment of the C-terminal domain of RNase E in complex with E. coli polynucleotide phosphorylase [Nurmohamed09], and with enolase [Nurmohamed10].

Both RrnA and CspE bind and inhibit RNase E, and T7 gene 0.7 protein kinase phosphorylates its carboxy-terminal half, stabilizing T7 mRNAs against RNase E degradation [Lee03d, Feng01a, Marchand01]. Ribosomal protein L4 interacts with the C-terminal region of RNase E inhibiting its activity, which may regulate the production of stress-induced proteins [Singh09]. The ATP-dependent RNA helicase RhlB binds to RNaseE as part of the degradosome, unwinding double stranded RNA for RNase E degradation. The minimal region on RNase E for RhlB recognition was mapped to RNase E residues 698-762. In addition, residues 628-843 and 694-790 stimulate the RhlB unwinding activity [Chandran07]. Co-expression of RNase E residues 696-762 and RhlB using a di-cistronic vector followed by biophysical study of their interaction demonstrated an avid binding between them [Worrall08].

Analysis of intragenic second-site suppressors of temperature-sensitive RNase E mutants demonstrated dissociation of the in vivo activity of RNase E on mRNA versus tRNA and rRNA substrates [Perwez08]. Substrate recognition determinants have been analyzed by site-directed mutagenesis [Garrey09] and the effect of a hyperactive N-terminal Q36R mutant of RNase E on RNA binding was studied [Go11]. Deletion analysis mapped the C-terminal Hfq binding region of RNase E which targets the degradation of mRNAs mediated by Hfq/sRNAs [Ikeda11]. Analysis of mutants in the 5'-phosphate sensor domain of RNase E suggested overlapping mechanisms of substrate recognition and a hierarchy of efficiencies toward target RNAs [Garrey11]. Other mutant studies showed that two RNA binding sites in the N-terminal domain of RNase E modulate its activity [Kim14].

Electron microscopy studies suggest that the degradosome binds to the cytoplasmic membrane via the N-terminal region of RNase E [Liou01]. The binding of the N-terminal catalytic domain of RNase E to the E. coli plasma membrane enhances stability and substrate affinity [Murashko12]. A segment of RNase E comprising residues 568-582 at the start of the C-terminal non-catalytic region has also been identified as being involved in membrane binding [Khemici08]. Evidence has been presented for the subcellular localization of RNase E and other components of the RNA processing and degradation network in extended cytoskeletal-like structures around the periphery of the cell [Taghbalout14, Taghbalout08, Taghbalout07]. However, contradictory work using live cell microscopy showed that RNase E is anchored to the inner cytoplasmic membrane via a membrane targeting sequence, but is not in cytoskeletal-like structures and is mobile on the membrane surface [Strahl15].

RNase E is required for cell division to occur [Goldblum81]. Inviability of rne mutants may be due to reduced levels of the cell-division protein FtsZ [Takada05]. The growth defect associated with RNase E mutants can be complemented by certain single amino acid substitutions in its paralog RNase G, although mRNA and tRNA metabolism is abnormal [Chung10]. The lethality of an RNase E mutant lacking its C-terminal half in combination with an rppH deletion is suppressed by rho or nusG mutants defective in Rho-dependent transcription termination [Anupama11]. Multiple chromosomal second-site suppressor mutations that restore colony forming ability to an RNase E deletion mutant have been identified, such as those in deaD [Tamura12]. RNase E deficiency also has effects on nutrient utilization by E. coli [Tamura13]. RNase E has a role in modulation of the bacterial SOS response that leads to transient arrest of cell division and initiation of DNA repair [Manasherob12].

The previously reported RNase K appears to be a proteolytic fragment of RNase E [Mudd93].

RNase E is of interest as a drug target because homologs are found in many different bacteria but not in humans or animals. Small molecule inhibitors of E. coli and Mycobacterium tuberculosis RNase E and RNase G have been reported [Kime15].

Reviews: [AitBara15, Bandyra13, Morita11, Kaberdin11, Bouvier11, Carpousis09, Carpousis07, Kushner02, Kennell02, Cohen97]

Citations: [Kemmer06, Takada07, Mackie08, Kime08, Stead11, AitBara15a]

Locations: cytosol, inner membrane

Map Position: [1,141,182 <- 1,144,367]

Molecular Weight of Polypeptide: 118.2 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0003668, CGSC:269, DIP:DIP-10727N, DisProt:DP00207, EchoBASE:EB0852, EcoGene:EG10859, EcoliWiki:b1084, Mint:MINT-1220086, ModBase:P21513, OU-Microarray:b1084, PortEco:rne, PR:PRO_000023789, Pride:P21513, Protein Model Portal:P21513, RefSeq:NP_415602, RegulonDB:EG10859, SMR:P21513, String:511145.b1084, UniProt:P21513

Relationship Links: InterPro:IN-FAMILY:IPR003029, InterPro:IN-FAMILY:IPR004659, InterPro:IN-FAMILY:IPR012340, InterPro:IN-FAMILY:IPR019307, InterPro:IN-FAMILY:IPR021968, InterPro:IN-FAMILY:IPR022967, InterPro:IN-FAMILY:IPR028878, PDB:Structure:1SLJ, PDB:Structure:1SMX, PDB:Structure:1SN8, PDB:Structure:2BX2, PDB:Structure:2C0B, PDB:Structure:2C4R, PDB:Structure:2FYM, PDB:Structure:2VMK, PDB:Structure:2VRT, PDB:Structure:3GCM, PDB:Structure:3GME, PDB:Structure:3H1C, PDB:Structure:3H8A, Pfam:IN-FAMILY:PF00575, Pfam:IN-FAMILY:PF10150, Pfam:IN-FAMILY:PF12111, Prosite:IN-FAMILY:PS50126, Smart:IN-FAMILY:SM00316

Gene-Reaction Schematic

Expand/Contract the Schematic connections:

Gene-Reaction Schematic


GO Terms:
Biological Process:
Inferred from experimentGO:0000967 - rRNA 5'-end processing [Li99b]
Inferred from experimentGO:0006401 - RNA catabolic process [Cormack93]
Inferred from experimentInferred by computational analysisGO:0006402 - mRNA catabolic process [Babitzke91, GOA06]
Inferred from experimentInferred by computational analysisGO:0008033 - tRNA processing [Li02, UniProtGOA11a, GOA06]
Inferred from experimentGO:0051289 - protein homotetramerization [Callaghan03]
Inferred by computational analysisGO:0006364 - rRNA processing [UniProtGOA11a, GOA06]
Inferred by computational analysisGO:0006396 - RNA processing [GOA01a]
Inferred by computational analysisGO:0090305 - nucleic acid phosphodiester bond hydrolysis [UniProtGOA11a]
Inferred by computational analysisGO:0090501 - RNA phosphodiester bond hydrolysis [GOA01a, Gaudet10]
Inferred by computational analysisGO:0090502 - RNA phosphodiester bond hydrolysis, endonucleolytic [GOA06]
Molecular Function:
Inferred from experimentInferred by computational analysisGO:0000287 - magnesium ion binding [Callaghan05, GOA06]
Inferred from experimentGO:0005515 - protein binding [Chandran07, Carpousis94, Py96, Erce10, AitBara10, Butland05, Regonesi06, Callaghan04]
Inferred from experimentInferred by computational analysisGO:0008270 - zinc ion binding [Callaghan05a, GOA06]
Inferred from experimentInferred by computational analysisGO:0008995 - ribonuclease E activity [Feng02, GOA01a]
Inferred by computational analysisGO:0003676 - nucleic acid binding [GOA01a]
Inferred by computational analysisGO:0003723 - RNA binding [UniProtGOA11a, GOA06, GOA01a]
Inferred by computational analysisGO:0004518 - nuclease activity [UniProtGOA11a]
Inferred by computational analysisGO:0004519 - endonuclease activity [UniProtGOA11a]
Inferred by computational analysisGO:0004521 - endoribonuclease activity [GOA06]
Inferred by computational analysisGO:0004540 - ribonuclease activity [GOA01a, Gaudet10]
Inferred by computational analysisGO:0016787 - hydrolase activity [UniProtGOA11a]
Inferred by computational analysisGO:0046872 - metal ion binding [UniProtGOA11a]
Cellular Component:
Inferred from experimentInferred by computational analysisGO:0009898 - cytoplasmic side of plasma membrane [Khemici08, Liou01, GOA06]
Inferred by computational analysisGO:0005737 - cytoplasm [UniProtGOA11, UniProtGOA11a, GOA06]
Inferred by computational analysisGO:0005886 - plasma membrane [UniProtGOA11, UniProtGOA11a, Miczak91]
Inferred by computational analysisGO:0016020 - membrane [UniProtGOA11a]

MultiFun Terms: information transferRNA relatedRNA degradation
metabolismdegradation of macromoleculesRNA

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number: 3.1.26.12

9S rRNA + 2 H2O → 5S rRNA + 2 an rRNA fragment

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number: 3.1.26.12

RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n an mRNA fragment

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number: 3.1.26.12

a polycistronic tRNA precursor + H2O → a tRNA precursor with a 5' extension and a short 3' extension + a partially processed polycistronic tRNA precursor

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA processing

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number: 3.1.26.12

a polycistronic tRNA precursor + H2O → a tRNA precursor with a 5' extension and a long 3' trailer + a partially processed polycistronic tRNA precursor

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

In Pathways: tRNA processing

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Enzymatic reaction of: ribonuclease

Inferred from experiment

EC Number: 3.1.26.12

RNase E degradation substrate mRNA + n H2O → n+1 an mRNA fragment

The direction shown, i.e. which substrates are on the left and right sides, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Subunit of: degradosome

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of degradosome = [(Ppk)2][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2]
         polyphosphate kinase = (Ppk)2 (extended summary available)
         ribonuclease E = (Rne)4 (extended summary available)
                 RNase E = Rne
         RhlB, ATP-dependent RNA helicase of the RNA degradosome = (RhlB)2 (extended summary available)
         polynucleotide phosphorylase = (Pnp)3 (extended summary available)
                 polynucleotide phosphorylase monomer = Pnp
         enolase = (Eno)2 (extended summary available)

Summary:
The degradosome is a large, multiprotein complex involved in RNA degradation. It consists of the RNA degradation enzymes RNase E and PNPase, as well as the ATP-dependent RNA helicase RhlB and the metabolic enzyme enolase [Py94, Carpousis94, Py96]. Polyphosphate kinase and the chaperone protein DnaK are also associated with and may be components of the degradosome [Blum97, Miczak96]. A "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible for this test case, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur [Coburn99]. Based on immunogold labeling studies, RhlB and RNase E are present in equimolar quantities in the degradosome, which is tethered to the cytoplasmic membrane via the amino-terminus of RNase E [Liou01].

RNase E provides the organizational structure for the degradosome. Its carboxy-terminal half binds PNPase, RhlB and enolase, and the loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I [Kido96, Vanzo98, Morita04]. This scaffold region is flexible, with isolated segments of increased structure that may be involved in binding other degradosome constituents [Callaghan04]. RNase E binding to partner proteins can be selectively disrupted. Loss of RhlB and enolase binding results in reduced degradosome activity. Conversely, disrupted PNPase binding yields increased activity. Strains any alteration in RNase E binding do not grow as well as wild type [Leroy02]. The amino-terminal half of RNase E contains sequences involved in oligomerization [Vanzo98].

In vitro purified degradosome generates 147-nucleotide RNase E cleavage intermediates from rpsT mRNA. Continuous cycles of polyadenylation and PNPase cleavage are necessary and sufficient to break down these intermediates, though RNase II can block this second degradation step [Coburn98]. RNAs with 3' REP stabilizers or stem loops must be polyadenylated to allow breakdown by the degradosome [Khemici04, Blum99]. Poly(G) and poly(U) tails do not allow degradation, though addition of a stretch of mixed nucleotides copied from within a coding region has stimulated degradation of a test substrate [Blum99].

The degradosome copurifies with fragments from its RNA substrates, including rRNA fragments derived from cleavage of 16S and 23S rRNA by RNase E, 5S rRNA and ssrA RNA [Bessarab98, LinChao99].

The DEAD-box helicases SrmB, RhlE and CsdA bind RNase E in vitro at a different site than RhlB. RhlE and CsdA can both replace RhlB in promoting PNPase activity in vitro [Khemici04a]. CsdA is induced by cold shock, and following a shift to 15 degrees C it copurifies with the degradosome [PrudhommeGenere04].

At least two poly(A)-binding proteins interact with the degradosome. The cold-shock protein CspE inhibits internal cleavage and breakdown of polyadenylated RNA by RNase E and PNPase by blocking digestion through the poly(A) tail. S1, a component of the 30S ribosome, binds to RNase E and PNPase without apparent effect on their activities [Feng01a].

The global effects of mutations in degradosome constituents on mRNA levels have been evaluated using microarrays [Bernstein04].

The degradosome has been reconstituted from recombinant components RNase E, RhlB, PNPase and enolase, purified and analyzed biochemically and biophysically. When compared with endogenously expressed degradosome extracted from cells using FLAG-tagged RNase E, data suggested that RNA may modulate the interaction of additional proteins with the degradosome [Worrall08a]. The degradosome associates stably with the 70S ribosome and polysomes, which may recruit degradosomes to translation sites [Tsai12]. RNase II is also associated with the degradosome [Lu14b].

Proteomic studies of the response to mutants in degradosome components RhlB, enolase, PNPase, or RNase E revealed the role of the degradosome in modulating the proteomic response to perturbations in this major RNA degradation pathway [Zhou13a].

Fluorescence microscopy imaging and fluorescence energy transfer measurements produced a model for the degradosome in which interactions between its major components are spatially defined [DominguezMalfav13]. Fluorescence microscopy techniques also show that in E. coli cells the degradosome components RNase E, RhlB, PNPase and enolase are organized into helical filaments coiled around the periphery of the cell in a cytoskeletal-like structure ( [Taghbalout07, Taghbalout08, Taghbalout14] and commented in [Hoch14]). However, a subsequent publication using fluorescence microscopy to visualize RhlB and RNase E under live cell conditions demonstrated their membrane association, but no cytoskeletal-like structures were observed [Strahl15].

Review: [Kaberdin11]

Locations: inner membrane


GO Terms:
Cellular Component:
GO:0005886 - plasma membrane [Liou01]

Credits:
Imported from EcoCyc 15-Mar-2016 by Paley S, SRI International


Sequence Features

Feature Class Location Citations Comment
Conserved-Region 39 -> 119
Inferred by computational analysis[UniProt15]
UniProt: S1 motif.
Mutagenesis-Variant 57
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by over 98%.
Protein-Segment 57 -> 112
Author statement[UniProt15]
UniProt: Interaction with RNA; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 66
Inferred from experiment[Schubert04]
UniProt: Disrupts folding of the S1 motif.
Mutagenesis-Variant 67
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by over 98%. Reduces affinity for RNA.
Mutagenesis-Variant 112
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by 98%. Loss of RNA-binding.
Protein-Segment 169 -> 170
Author statement[UniProt15]
UniProt: Interaction with RNA 5'-terminal monophosphate; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 170
Inferred from experiment[Kime10, Callaghan05]
UniProt: Abolishes enzyme activity toward RNA substrates with a 5' monophosphate (PubMed:16237448). Strongly reduces enzyme activity toward cspA mRNA (PubMed:19889093).
Mutagenesis-Variant 303
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by over 96%.
Metal-Binding-Site 303
Author statement[UniProt15]
UniProt: Magnesium; catalytic.
Mutagenesis-Variant 305
Inferred from experiment[Callaghan05]
D or L: Reduces RNA cleavage by over 96%.
Mutagenesis-Variant 346
Inferred from experiment[Callaghan05]
UniProt: Reduces RNA cleavage by over 96%. Reduces affinity for RNA.
Metal-Binding-Site 346
Author statement[UniProt15]
UniProt: Magnesium; catalytic.
Mutagenesis-Variant 373
Inferred from experiment[Callaghan05]
A or D: Reduces RNA cleavage by 89%.
Sequence-Conflict 390
Inferred by curator[ClaverieMartin91, UniProt15]
UniProt: (in Ref. 5; AAA23443).
Mutagenesis-Variant 404
Inferred from experiment[Callaghan05a]
UniProt: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity.
Metal-Binding-Site 404
Author statement[UniProt15]
UniProt: Zinc; shared with dimeric partner.
Protein-Segment 404 -> 407
Author statement[UniProt15]
UniProt: Required for zinc-mediated homotetramerization and catalytic activity; Sequence Annotation Type: region of interest.
Mutagenesis-Variant 407
Inferred from experiment[Callaghan05a]
UniProt: Reduces zinc-binding. Abolishes homotetramerization and enzyme activity.
Metal-Binding-Site 407
Author statement[UniProt15]
UniProt: Zinc; shared with dimeric partner.
Sequence-Conflict 487
Inferred by curator[ClaverieMartin91, Casaregola92, UniProt15]
UniProt: (in Ref. 4; CAA47818 and 5; AAA23443).
Sequence-Conflict 564
Inferred by curator[Casaregola92, UniProt15]
UniProt: (in Ref. 4; CAA47818).
Sequence-Conflict 784
Inferred by curator[Casaregola92, UniProt15]
UniProt: (in Ref. 4; CAA47818).
Protein-Segment 833 -> 850
Author statement[UniProt15]
UniProt: Interaction with enolase; Sequence Annotation Type: region of interest.
Sequence-Conflict 838
Inferred by curator[ClaverieMartin91, UniProt15]
UniProt: (in Ref. 5; AAA23443).
Sequence-Conflict 905
Inferred by curator[Casaregola92, UniProt15]
UniProt: (in Ref. 4; CAA47818).
Protein-Segment 1021 -> 1061
Author statement[UniProt15]
UniProt: Interaction with PNPase; Sequence Annotation Type: region of interest.
Sequence-Conflict 1048
Inferred by curator[Cormack93, UniProt15]
UniProt: (in Ref. 7; AAA03347).


Sequence Pfam Features

Feature Class Location Citations Comment
Pfam PF00575 36 -> 118
Inferred by computational analysis[Finn14]
S1 : S1 RNA binding domain [More...]
Pfam PF10150 121 -> 391
Inferred by computational analysis[Finn14]
RNase_E_G : Ribonuclease E/G family [More...]
Pfam PF12111 1022 -> 1058
Inferred by computational analysis[Finn14]
PNPase_C : Polyribonucleotide phosphorylase C terminal [More...]


References

Afonyushkin05: Afonyushkin T, Vecerek B, Moll I, Blasi U, Kaberdin VR (2005). "Both RNase E and RNase III control the stability of sodB mRNA upon translational inhibition by the small regulatory RNA RyhB." Nucleic Acids Res 33(5);1678-89. PMID: 15781494

AitBara10: Ait-Bara S, Carpousis AJ (2010). "Characterization of the RNA degradosome of Pseudoalteromonas haloplanktis: conservation of the RNase E-RhlB interaction in the gammaproteobacteria." J Bacteriol 192(20);5413-23. PMID: 20729366

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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