eF-site ID 4q4z-ABCDEF PDB Code 4q4z Chain A, B, C, D, E, F Title Thermus thermophilus RNA polymerase de novo transcription initiation complex Classification transcription/DNA 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 KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFH TGGITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEE KLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRG AIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHI EIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLI AEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLT EAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVD QKTLKAIEEARKEA E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP EDRLQKEMERLYPV F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS EITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKA LSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERI RQIENKALRKLKYHESRTRKLRDFLD Description Functional site 1) chain C residue 567 type sequence Q description BINDING SITE FOR RESIDUE ATP C 1201 source : AC1 2) chain C residue 838 type sequence K description BINDING SITE FOR RESIDUE ATP C 1201 source : AC1 3) chain C residue 999 type sequence H description BINDING SITE FOR RESIDUE ATP C 1201 source : AC1 4) chain D residue 704 type sequence R description BINDING SITE FOR RESIDUE ATP C 1201 source : AC1 5) chain D residue 743 type sequence D description BINDING SITE FOR RESIDUE ATP C 1201 source : AC1 6) chain D residue 1112 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC2 7) chain D residue 1194 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC2 8) chain D residue 1201 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC2 9) chain D residue 1204 type sequence C description BINDING SITE FOR RESIDUE ZN D 2001 source : AC2 10) chain D residue 58 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC3 11) chain D residue 60 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC3 12) chain D residue 73 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC3 13) chain D residue 76 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC3 14) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC4 15) chain D residue 741 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC4 16) chain D residue 743 type sequence D description BINDING SITE FOR RESIDUE MG D 2003 source : AC4 17) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2004 source : AC5 18) chain D residue 840 type sequence K description BINDING SITE FOR RESIDUE MG D 2005 source : AC6 19) chain C residue 557 type sequence R description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 20) chain C residue 879 type sequence R description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 21) chain D residue 704 type sequence R description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 22) chain D residue 706 type sequence P description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 23) chain D residue 737 type sequence N description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 24) chain D residue 1029 type sequence R description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 25) chain D residue 1235 type sequence Q description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 26) chain D residue 1238 type sequence M description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 27) chain D residue 1240 type sequence T description BINDING SITE FOR RESIDUE 2TM D 2006 source : AC7 28) chain D residue 1201 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 29) chain D residue 1204 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 30) chain D residue 739 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 31) chain D residue 741 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 32) chain D residue 743 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 33) chain D residue 1112 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 34) chain D residue 1194 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 35) chain D residue 76 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 36) chain D residue 58 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 37) chain D residue 60 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 38) chain D residue 73 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 39) chain C residue 836-848 type prosite sequence GDKLANRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKLANrHGNKGV source prosite : PS01166 40) chain F residue 382-408 type prosite sequence TLEEVGAFFGVTRERIRQIENKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL source prosite : PS00716 41) chain F residue 187-194 type prosite sequence LIEANLRL description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL source prosite : PS00867

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