>TIGR01461 greB transcription elongation factor GreB; InterPro: IPR006358 Bacterial GreA IPR006359 from INTERPRO and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase, allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue preexisting arrested complexes . A 15 Å resolution helical reconstruction of the Escherichia coli core RNA polymerase (RNAP)/GreB complex that allows fitting of high-resolution RNAP and GreB structures. The model of the complex reveals a remarkable binding mode for GreB; the globular C-terminal domain binds RNAP at the edge of the active site channel, while the N-terminal coiled-coil domain extends 45 Å into a channel directly to the RNAP active site. The results point to a key role for conserved acidic residues at the tip of the Gre factor coiled coil in modifying the RNAP active site to catalyse the transcript cleavage reaction, and mutational studies confirm that these positions are critical for Gre factor function. Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil.; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.

Probab=100.00 E-value=0 Score=316.84 Aligned_cols=154 Identities=36% Similarity=0.563 Sum_probs=150.5 Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC Q ss_conf 43148899999999999998724899999999997517622243048999887687999999997444421047210133 Q gi|254780440|r 4 KIPVTSKGFDKIQQELRWRQQEERPRIIKAISEARAYGDLSENAEYQAAKELQNLNEGRMAELENIITRAEVIDISTMSG 83 (158) Q Consensus 4 k~~lT~~g~~~L~~El~~l~~~~r~~~~~~i~~A~~~GDl~ENaeY~aAke~q~~~~~ri~~L~~~L~~A~iv~~~~~~~ 83 (158) T Consensus 2 ~pliTpeG~~~Lk~EL~~Lw~~eRPevtq~V~wAA~lGDRSENadY~YgKkrlREIDrRvRfLtKrLEnlkvVd~~p~~~ 81 (157) T TIGR01461 2 TPLITPEGYEKLKDELYELWRKERPEVTQIVSWAAALGDRSENADYLYGKKRLREIDRRVRFLTKRLENLKVVDEEPREA 81 (157) T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCEECCCCCCCC T ss_conf 88717878999999999886232862113232442168712242100166000022112446555443001117653554 Q ss_pred -CCCCCCCEEEEEECCCCCEEEEEEECHHHCCCCCCEECCCCHHHHHHCCCCCCCEEEEECCCCEEEEEEEEEEEC Q ss_conf -211136579995347652359999631013345881501317899872888887899982897199999998979 Q gi|254780440|r 84 -DRIAFGATVSLVEKNSGDKKNYQIVGDQEADVQSGLVSISSPIARALIGKELGDIISVNAPGGEKTYEILQVLWI 158 (158) Q Consensus 84 -~~V~~Gs~V~l~d~~~~~~~~~~lVg~~e~d~~~~~IS~~SPlG~ALlG~~~Gd~V~v~~p~G~~~~~Il~I~yi 158 (158) T Consensus 82 t~~VfFGAwV~le~-~DG~~~r~rIVG~DEid~r~n~ISidSPlARaL~kke~gdevvvnTPaGe~~~~v~~iEY~ 156 (157) T TIGR01461 82 TDKVFFGAWVELED-DDGREQRYRIVGIDEIDTRKNKISIDSPLARALIKKEVGDEVVVNTPAGEEEWYVLSIEYV 156 (157) T ss_pred CCCEEEEEEEEEEC-CCCCCCCEEEEECCCCCCCCCCEEEECHHHHHHHCCCCCCEEEEECCCCCCEEEEEEEEEC T ss_conf 57677225888653-8883202688605521235772014266788863012587778757888504788875206

HHsearch alignment for GI: 254780440 and conserved domain: TIGR01461