eF-site ID 4q5s-ABCDEFGHI PDB Code 4q5s Chain A, B, C, D, E, F, G, H, I Title Thermus thermophilus RNA polymerase initially transcribing complex containing 6-mer RNA Classification transcription/DNA/rna 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:  EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDG LFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTKS IVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATEL EQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRY GKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVA LYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILA ELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATYF LPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQVE AEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEA GDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPF EDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNV VRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKH PSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPD LRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAP EIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSL TDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCG LPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDI KDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEG QSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQM LSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAG LEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVF ANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFA RIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLG MEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQY LEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKV TQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRG LMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGAD TALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLF QPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEG RYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQK CYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMQGLPR VIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEG FSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEA KGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKY VEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWK PLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDE LIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEA RKEA E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP EDRLQKEMERLYPV F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS EITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL ETPFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSER EAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQIENKA LRKLKYHESRTRKLRDFL G:  TGCATCCGTGAGTG H:  TATAATGGGGGATGCA I:  CUCAC Description Functional site 1) chain D residue 739 type sequence D description BINDING SITE FOR RESIDUE MG D 2001 source : AC1 2) chain D residue 741 type sequence D description BINDING SITE FOR RESIDUE MG D 2001 source : AC1 3) chain D residue 743 type sequence D description BINDING SITE FOR RESIDUE MG D 2001 source : AC1 4) chain I residue 5 type sequence A description BINDING SITE FOR RESIDUE MG D 2001 source : AC1 5) chain I residue 6 type sequence C description BINDING SITE FOR RESIDUE MG D 2001 source : AC1 6) chain D residue 58 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 7) chain D residue 60 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 8) chain D residue 73 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 9) chain D residue 76 type sequence C description BINDING SITE FOR RESIDUE ZN D 2002 source : AC2 10) chain D residue 1112 type sequence C description BINDING SITE FOR RESIDUE ZN D 2003 source : AC3 11) chain D residue 1194 type sequence C description BINDING SITE FOR RESIDUE ZN D 2003 source : AC3 12) chain D residue 1201 type sequence C description BINDING SITE FOR RESIDUE ZN D 2003 source : AC3 13) chain D residue 1204 type sequence C description BINDING SITE FOR RESIDUE ZN D 2003 source : AC3 14) chain C residue 390 type sequence Q description BINDING SITE FOR RESIDUE ATP I 101 source : AC4 15) chain C residue 420 type sequence R description BINDING SITE FOR RESIDUE ATP I 101 source : AC4 16) chain G residue 14 type sequence G description BINDING SITE FOR RESIDUE ATP I 101 source : AC4 17) chain G residue 15 type sequence T description BINDING SITE FOR RESIDUE ATP I 101 source : AC4 18) chain I residue 2 type sequence C description BINDING SITE FOR RESIDUE ATP I 101 source : AC4 19) chain F residue 382-408 type prosite sequence TLEEVGAFFGVTRERIRQIENKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL source prosite : PS00716 20) chain F residue 187-194 type prosite sequence LIEANLRL description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL source prosite : PS00867 21) chain C residue 836-848 type prosite sequence GDKLANRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKLANrHGNKGV source prosite : PS01166 22) chain D residue 58 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 23) chain D residue 1201 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 24) chain D residue 1204 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 25) chain D residue 60 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 26) chain D residue 73 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 27) chain D residue 76 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 28) chain D residue 739 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 29) chain D residue 741 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 30) chain D residue 743 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 31) chain D residue 1112 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 32) chain D residue 1194 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1

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