eF-site ID 4oip-ABCDEF PDB Code 4oip Chain A, B, C, D, E, F Title Crystal structure of Thermus thermophilus transcription initiation complex soaked with GE23077, ATP, and CMPcPP 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 KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTITQGL PRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVES EGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLL EAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMM KYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVA WKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKK DELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIE EARKEA E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP EDRLQKEMERLYPV F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS EITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKA LSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERI RQIENKALRKLKYHESRTRKLRDFLD Description Functional site 1) chain B residue 183 type sequence D description BINDING SITE FOR RESIDUE MG B 2001 source : AC1 2) chain B residue 191 type sequence D description BINDING SITE FOR RESIDUE MG B 2001 source : AC1 3) chain B residue 193 type sequence D description BINDING SITE FOR RESIDUE MG B 2001 source : AC1 4) chain D residue 1112 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC2 5) chain D residue 1194 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC2 6) chain D residue 1201 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC2 7) chain D residue 1204 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC2 8) chain D residue 58 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC3 9) chain D residue 60 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC3 10) chain D residue 73 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC3 11) chain D residue 76 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC3 12) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC4 13) chain D residue 741 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC4 14) chain D residue 743 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC4 15) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2004 source : AC5 16) chain B residue 168 type sequence D description BINDING SITE FOR RESIDUE MG D 2005 source : AC6 17) chain D residue 840 type sequence K description BINDING SITE FOR RESIDUE MG D 2005 source : AC6 18) chain D residue 897 type sequence W description BINDING SITE FOR RESIDUE MG D 2006 source : AC7 19) chain D residue 900 type sequence I description BINDING SITE FOR RESIDUE MG D 2006 source : AC7 20) chain C residue 878 type sequence S description BINDING SITE FOR RESIDUE ATP D 2007 source : AC8 21) chain C residue 879 type sequence R description BINDING SITE FOR RESIDUE ATP D 2007 source : AC8 22) chain D residue 783 type sequence R description BINDING SITE FOR RESIDUE ATP D 2007 source : AC8 23) chain D residue 1029 type sequence R description BINDING SITE FOR RESIDUE ATP D 2007 source : AC8 24) chain F residue 292 type sequence A description BINDING SITE FOR RESIDUE MG F 2001 source : AC9 25) chain F residue 296 type sequence G description BINDING SITE FOR RESIDUE MG F 2001 source : AC9 26) chain F residue 299 type sequence W description BINDING SITE FOR RESIDUE MG F 2001 source : AC9 27) chain A residue 54 type sequence T description BINDING SITE FOR GE23077 source : BC1 28) chain A residue 146 type sequence R description BINDING SITE FOR GE23077 source : BC1 29) chain A residue 158 type sequence I description BINDING SITE FOR GE23077 source : BC1 30) chain A residue 171 type sequence F description BINDING SITE FOR GE23077 source : BC1 31) chain B residue 8 type sequence A description BINDING SITE FOR GE23077 source : BC1 32) chain B residue 189 type sequence R description BINDING SITE FOR GE23077 source : BC1 33) chain C residue 444 type sequence P description BINDING SITE FOR GE23077 source : BC1 34) chain C residue 445 type sequence E description BINDING SITE FOR GE23077 source : BC1 35) chain C residue 448 type sequence N description BINDING SITE FOR GE23077 source : BC1 36) chain C residue 557 type sequence R description BINDING SITE FOR GE23077 source : BC1 37) chain C residue 560 type sequence M description BINDING SITE FOR GE23077 source : BC1 38) chain C residue 563 type sequence N description BINDING SITE FOR GE23077 source : BC1 39) chain C residue 567 type sequence Q description BINDING SITE FOR GE23077 source : BC1 40) chain C residue 838 type sequence K description BINDING SITE FOR GE23077 source : BC1 41) chain C residue 846 type sequence K description BINDING SITE FOR GE23077 source : BC1 42) chain D residue 58 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 43) chain D residue 1201 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 44) chain D residue 1204 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 45) chain D residue 60 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 46) chain D residue 73 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 47) chain D residue 76 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 48) chain D residue 739 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 49) chain D residue 741 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 50) chain D residue 743 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 51) chain D residue 1112 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 52) chain D residue 1194 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 53) chain F residue 382-408 type prosite sequence TLEEVGAFFGVTRERIRQIENKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL source prosite : PS00716 54) chain F residue 187-194 type prosite sequence LIEANLRL description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL source prosite : PS00867 55) 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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