>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659 The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are: Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO Associated components: The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP. Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2] In vitro 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, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. 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 , , . Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too. RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.

Probab=100.00 E-value=0 Score=1139.00 Aligned_cols=453 Identities=43% Similarity=0.680 Sum_probs=412.3 Q ss_pred EEEEEEEE-CCEEEEEEECCCCCCCCCCCEEEEEEEEECCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCHHHHHHHHHH Q ss_conf 07999998-99899999607334604287879899783638823135327897713022213712102898899999998 Q gi|254780751|r 14 ETRVVVLR-DNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIPFSDRQALLKE 92 (723) Q Consensus 14 e~Rvav~e-~g~l~e~~~e~~~~~~~~GnIY~G~V~~V~p~lqAAFVdiG~~k~gFL~~~ei~~~y~~ip~~d~~~l~~~ 92 (723) T Consensus 1 e~r~Al~~~~~~l~el~ier~~~~~~~GnIY~G~V~~vlPsl~AAFvdiG~~~~GFLh~sdi~~~~~~~~~~~~~----- 75 (464) T TIGR00757 1 ETRVALVELGGQLQELIIERPKSRQLVGNIYKGRVTRVLPSLQAAFVDIGLEKNGFLHASDIGENSEKLEQLVDT----- 75 (464) T ss_pred CEEEEEEEECCEEEEEEEECCHHHCCHHHHHHCEEEEECCCCCEEEEECCCCCCCCCCHHHCCCCHHHHHHHHHC----- T ss_conf 958999961877999998431110110023202020220376447742068835563033203324568888620----- Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE Q ss_conf 88631111100000001112233444334454222233445543322223432112211121100001223444421331 Q gi|254780751|r 93 SNIAQTDSEAVADDVTHGDVTIPNDHSLEEVAPIANFSQETEEESIISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQE 172 (723) Q Consensus 93 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 172 (723) T Consensus 76 d~~-----------------------NA~~~a~~~~-----------~~~~~~~~kp~~~~QS~~~~~~~~~~~~~~I~e 121 (464) T TIGR00757 76 DDD-----------------------NAEAEAAPAE-----------AKREAGQEKPEEIIQSSGDELERRQSKTASISE 121 (464) T ss_pred CCC-----------------------CCCCCCCHHH-----------HHHHHHCCCCHHHHCCCHHHHHHHHCCCCCHHH T ss_conf 212-----------------------5767788233-----------220100136213202530245543135435266 Q ss_pred CCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCEEEECCCCHHHHHHHHHHHHHHHCCCC--CEEEEE Q ss_conf 068885799984033323456410123345765234422788751242046886899999999986300258--716998 Q gi|254780751|r 173 VIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEIARGLEVPAG--MGVILR 250 (723) Q Consensus 173 ~lk~gq~ilVQV~ke~~~~Kga~lT~~isl~Gry~Vl~P~~~~~~~iSrki~~~~~r~~l~~~~~~~~~~~~--~G~IiR 250 (723) T Consensus 122 ~L~~gq~vlVQV~Kep~G~KGArLTt~ISlpGrYlVlmP~~~~~~g~SRri~~~~eR~rLK~~~~~~~~p~~nt~G~IiR 201 (464) T TIGR00757 122 LLRPGQSVLVQVVKEPRGNKGARLTTDISLPGRYLVLMPNTSHQVGVSRRIESEEERERLKKLLRSEVLPEGNTMGLIIR 201 (464) T ss_pred HHCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCEEEEEE T ss_conf 61288858999885267898873546622462107855788943203441288245899999999853888770468998 Q ss_pred EECCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCCHHHHHHHHHCCCCCCEEECCC----CCHHHHHHHHH Q ss_conf 5045575799999999999999987764201432212-345645888888752376631111035----32036678889 Q gi|254780751|r 251 TAGASRTKIEIKRDFEYLMRLWDNVRELALNSVAPHL-VYEEGNLIKRAIRDLYCKDISEIIVSG----EKGYREAKDFM 325 (723) Q Consensus 251 T~a~~~~~~~l~~d~~~L~~~w~~i~~~~~~~~~p~l-i~~~~~~~~~~ird~~~~~~~~i~vd~----~~~~~~~~~~~ 325 (723) T Consensus 202 Taa~g~~~~~l~~D~~~L~~~W~~i~~~~~~~~~p~l~l~~E~~~i~r~~rD~~~~~~~~i~id~PaG~~~~y~~~~~~~ 281 (464) T TIGR00757 202 TAAEGASEEELKKDLEELLRKWEKIKEKAQKRSAPILELYEEDDIIKRVLRDYLDTDVKEIVIDSPAGMKEIYEEIKEFI 281 (464) T ss_pred ECCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHH T ss_conf 40379998999999999999899999985047854101124504789999985101257789728610799999999985 Q ss_pred H-HHHHCCCCHHHHCCCCCH-HHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCEEEEEEECCCCCCCCCC-CHHHHHHH Q ss_conf 8-763101211220134420-35677699999998422214367864998328806999823755444555-11479999 Q gi|254780751|r 326 K-LLMPSYARIVRQYEDPHP-IFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHC-IEDTALQT 402 (723) Q Consensus 326 ~-~~~p~~~~~v~~~~~~~~-lf~~y~ie~~i~~~~~~~V~L~sGG~lvIe~TEALt~IDVNSG~~~~~~~-~e~t~l~t 402 (723) T Consensus 282 ~~~~~Pe~~~Kl~~y~~~~p~~F~~f~ie~~i~~a~~r~V~L~SGGyivId~TEAlt~IDVNSG~~t~~~~n~EET~~~t 361 (464) T TIGR00757 282 QDLVAPELVSKLKLYEGSLPPLFEGFQIEKQIEKALSRKVWLPSGGYIVIDQTEALTVIDVNSGRFTGKRNNLEETALNT 361 (464) T ss_pred HCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCCEEECCCCCEEEECCCCCEEEEEECCCHHHCCCCCCHHHHHHH T ss_conf 00147314541443037788766533368999998388575588878876587403787604503112578723568888 Q ss_pred HHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEECCCCCCCHHHHHCC Q ss_conf 99999999998731036863896033479888899999999997312787289986048614898515666301121002 Q gi|254780751|r 403 NLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTK 482 (723) Q Consensus 403 NleAA~EIaRQlRLRnlgGiIvIDFIdM~~~~~~~~v~~~l~~~l~~D~~~~~v~~it~lGLlEltRkR~r~sl~e~~~~ 482 (723) T Consensus 362 NLEAA~EiArQLrLRnlGGiiiiDFIDM~~~k~~~~vl~~l~~~l~~DraR~~i~~~s~lGLvEmTRkR~r~SL~e~~~~ 441 (464) T TIGR00757 362 NLEAAKEIARQLRLRNLGGIIIIDFIDMKSEKNRRRVLERLKEALSRDRARIQILGISELGLVEMTRKRLRESLMEVLGE 441 (464) T ss_pred HHHHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCHHHCCCHHHHHHHHHHCCCCHHHHHCC T ss_conf 89999999877521015847999510698866689999999999861663100110130103333042326743655247 Q ss_pred CCCCCCCEEEEECCHHHHHHHHH Q ss_conf 36754653786061146899887 Q gi|254780751|r 483 VCTYCKGAGYIRSQSSVALSILR 505 (723) Q Consensus 483 ~c~~c~g~g~~~~~~~~~~~~~r 505 (723) T Consensus 442 ~CP~C~G~G~v~~~e~~~~~i~R 464 (464) T TIGR00757 442 TCPHCSGRGIVKTSETVLLEIER 464 (464) T ss_pred CCCCCCCEEEEECCCCHHHHCCC T ss_conf 88874741278326500021029

HHsearch alignment for GI: 254780751 and conserved domain: TIGR00757