eF-site ID 4oio-ABCDEF PDB Code 4oio Chain A, B, C, D, E, F Title Crystal structure of Thermus thermophilus pre-insertion substrate complex for de novo transcription initiation Classification TRANSCRIPTION, TRANSFERASE Compound DNA-directed RNA polymerase subunit alpha Source ORGANISM_SCIENTIFIC: Thermus thermophilus; Sequence A:  SKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRI LLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLK ELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIM NPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRIN AIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDG SVTPLEALNQAVEILREHLTYFSNPQ B:  KAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLS SIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELV VRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPD LHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAIP VDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVT PLEALNQAVEILREHLTYFSNP C:  MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRE NVGIQAAFRETFPIEELVLDFLEYRLGEPPFPQDECREKD LTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSF IINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPK RGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETL ARELGAYGELVQGLMDESVFAMRPEEALIRLFTLLRPGDP PKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSG RTLARFEDGEFKDEVFLPTLRYLFALTAGVPGHEVDDIDH LGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSL TPAKLVNSRPLEAAIREFFSRSQLSQFKDETNPLSSLRHK RRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGA NIGLITSLAAYARVDELGFIRTPYRRVVGGVVTDEVVYMT ATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPE EVEFMDVSPKQVFSVNTNLIPFLEHDDANRALMGSNMQTQ AVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVD GNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQRPRVVVGQ RVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDA IVISEELLKRDFYTSIHIERYEIEARDTKLGPERITRDIP HLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEP TPEERLLRSIFGEKARDVKDTSLRVPPGEGGIVVRTVRLR RGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKG VVAKILPVEDMPHLPDGTPVDVILNPLGVPSRMNLGQILE THLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFG KRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPEEQLKELF LQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHA RSTGPYSLITQQPLGGKAQFGGQRFGEMEVWALEAYGAAH TLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRV LVKELQALALDVQTLDEKDNPVDIFEGLASK 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 FQPTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRY LSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCY GYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRQGLPRV IELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGF SKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAK GPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYV EVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKP LLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDEL IGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEA E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP EDRLQKEMERLYPV F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS EITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKA LSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERI RQIENKALRKLKYHESRTRKLRDF Description Functional site 1) chain D residue 1112 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC1 2) chain D residue 1194 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC1 3) chain D residue 1201 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC1 4) chain D residue 1204 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC1 5) chain D residue 58 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 6) chain D residue 60 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 7) chain D residue 73 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 8) chain D residue 76 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 9) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC3 10) chain D residue 741 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC3 11) chain D residue 743 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC3 12) chain C residue 685 type sequence E description BINDING SITE FOR RESIDUE MG D 2004 source : AC4 13) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2004 source : AC4 14) chain C residue 567 type sequence Q description BINDING SITE FOR RESIDUE ATP D 2005 source : AC5 15) chain C residue 838 type sequence K description BINDING SITE FOR RESIDUE ATP D 2005 source : AC5 16) chain C residue 846 type sequence K description BINDING SITE FOR RESIDUE ATP D 2005 source : AC5 17) chain C residue 998 type sequence Y description BINDING SITE FOR RESIDUE ATP D 2005 source : AC5 18) chain C residue 999 type sequence H description BINDING SITE FOR RESIDUE ATP D 2005 source : AC5 19) chain D residue 704 type sequence R description BINDING SITE FOR RESIDUE ATP D 2005 source : AC5 20) chain D residue 741 type sequence D description BINDING SITE FOR RESIDUE ATP D 2005 source : AC5 21) chain D residue 743 type sequence D description BINDING SITE FOR RESIDUE ATP D 2005 source : AC5 22) chain C residue 879 type sequence R description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC6 23) chain D residue 704 type sequence R description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC6 24) chain D residue 706 type sequence P description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC6 25) chain D residue 737 type sequence N description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC6 26) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC6 27) chain D residue 1029 type sequence R description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC6 28) chain D residue 58 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 29) chain D residue 1201 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 30) chain D residue 1204 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 31) chain D residue 60 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 32) chain D residue 73 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 33) chain D residue 76 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 34) chain D residue 739 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 35) chain D residue 741 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 36) chain D residue 743 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 37) chain D residue 1112 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 38) chain D residue 1194 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 39) chain F residue 382-408 type prosite sequence TLEEVGAFFGVTRERIRQIENKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL source prosite : PS00716 40) chain F residue 187-194 type prosite sequence LIEANLRL description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL source prosite : PS00867 41) 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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