eF-site ID 4oir-ABCDEFGH PDB Code 4oir Chain A, B, C, D, E, F, G, H Title Crystal structure of Thermus thermophilus RNA polymerase transcription initiation complex soaked with GE23077 and rifamycin SV Classification TRANSCRIPTION, TRANSFERASE/ANTIBIOTIC Compound DNA-directed RNA polymerase subunit alpha Source ORGANISM_SCIENTIFIC: Thermus thermophilus; Sequence A:  SKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRI LLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLK ELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIM NPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRIN AIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDG SVTPLEALNQAVEILREHLTYFSNPQAAAVA B:  LDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLR RILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILN LKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVE IMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDR INAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWT DGSVTPLEALNQAVEILREHLTYFSNP C:  MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRE NVGIQAAFRETFPIEEGLVLDFLEYRLGEPPFPQDECREK DLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGS FIINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLP KRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQET LARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGD PPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLS GRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDID HLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDS LTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRH KRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEG ANIGLITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYM TATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSP EEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQT QAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKV DGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVG QRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFED AIVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDI PHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESE PTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRL RRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNK GVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQIL ETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYF GKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKEL FLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMH ARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAA HTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFR VLVKELQALALDVQTLDEKDNPVDIFEGLASK D:  KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERD GLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTK SIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATE LEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELR YGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV ALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEIL AELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATY FLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQV EAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVE AGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYP FEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRN VVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMK HPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPP DLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGA PEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRS LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQC GLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRD IKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVE GQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQ MLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGA GLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYV FANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILF ARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRL GMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQ YLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK VTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLR GLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGA DTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPL FQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEE GRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQ KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMQGLP RVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESE GFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLE AKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMK YVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAW KPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKD ELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEE ARKEA E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP EDRLQKEMERLYPV F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS EITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKA LSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERI RQIENKALRKLKYHESRTRKLRDFLD G:  GCATCCGTGAGTCGAG H:  TATAATGGGAGCTGTCACGGATGC Description Functional site 1) chain B residue 154 type sequence E description BINDING SITE FOR RESIDUE MG B 401 source : AC1 2) chain B residue 168 type sequence D description BINDING SITE FOR RESIDUE MG B 401 source : AC1 3) chain D residue 840 type sequence K description BINDING SITE FOR RESIDUE MG B 401 source : AC1 4) chain C residue 390 type sequence Q description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 5) chain C residue 392 type sequence S description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 6) chain C residue 393 type sequence Q description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 7) chain C residue 394 type sequence F description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 8) chain C residue 405 type sequence R description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 9) chain C residue 406 type sequence H description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 10) chain C residue 409 type sequence R description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 11) chain C residue 411 type sequence S description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 12) chain C residue 420 type sequence R description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 13) chain C residue 448 type sequence N description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 14) chain C residue 452 type sequence I description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 15) chain F residue 323 type sequence D description BINDING SITE FOR RESIDUE RFV C 1201 source : AC2 16) chain D residue 1112 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC3 17) chain D residue 1194 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC3 18) chain D residue 1201 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC3 19) chain D residue 1204 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC3 20) chain D residue 58 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC4 21) chain D residue 60 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC4 22) chain D residue 73 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC4 23) chain D residue 76 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC4 24) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC5 25) chain D residue 741 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC5 26) chain D residue 743 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC5 27) chain D residue 897 type sequence W description BINDING SITE FOR RESIDUE MG D 2004 source : AC6 28) chain D residue 900 type sequence I description BINDING SITE FOR RESIDUE MG D 2004 source : AC6 29) chain F residue 292 type sequence A description BINDING SITE FOR RESIDUE MG F 2001 source : AC7 30) chain F residue 296 type sequence G description BINDING SITE FOR RESIDUE MG F 2001 source : AC7 31) chain F residue 299 type sequence W description BINDING SITE FOR RESIDUE MG F 2001 source : AC7 32) chain A residue 54 type sequence T description BINDING SITE FOR GE23077 source : AC8 33) chain A residue 146 type sequence R description BINDING SITE FOR GE23077 source : AC8 34) chain A residue 158 type sequence I description BINDING SITE FOR GE23077 source : AC8 35) chain A residue 171 type sequence F description BINDING SITE FOR GE23077 source : AC8 36) chain B residue 8 type sequence A description BINDING SITE FOR GE23077 source : AC8 37) chain B residue 9 type sequence P description BINDING SITE FOR GE23077 source : AC8 38) chain B residue 29 type sequence E description BINDING SITE FOR GE23077 source : AC8 39) chain B residue 189 type sequence R description BINDING SITE FOR GE23077 source : AC8 40) chain C residue 445 type sequence E description BINDING SITE FOR GE23077 source : AC8 41) chain C residue 446 type sequence G description BINDING SITE FOR GE23077 source : AC8 42) chain C residue 557 type sequence R description BINDING SITE FOR GE23077 source : AC8 43) chain C residue 560 type sequence M description BINDING SITE FOR GE23077 source : AC8 44) chain C residue 563 type sequence N description BINDING SITE FOR GE23077 source : AC8 45) chain C residue 567 type sequence Q description BINDING SITE FOR GE23077 source : AC8 46) chain C residue 838 type sequence K description BINDING SITE FOR GE23077 source : AC8 47) chain C residue 846 type sequence K description BINDING SITE FOR GE23077 source : AC8 48) chain G residue 17 type sequence G description BINDING SITE FOR GE23077 source : AC8 49) chain D residue 58 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 50) chain D residue 1201 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 51) chain D residue 1204 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 52) chain D residue 60 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 53) chain D residue 73 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 54) chain D residue 76 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 55) chain D residue 739 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 56) chain D residue 741 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 57) chain D residue 743 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 58) chain D residue 1112 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 59) chain D residue 1194 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 60) chain F residue 382-408 type prosite sequence TLEEVGAFFGVTRERIRQIENKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL source prosite : PS00716 61) chain F residue 187-194 type prosite sequence LIEANLRL description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL source prosite : PS00867 62) chain C residue 836-848 type prosite sequence GDKLANRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKLANrHGNKGV source prosite : PS01166

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