eF-site ID 1l9u-ABCDEH PDB Code 1l9u Chain A, B, C, D, E, H click to enlarge Title THERMUS AQUATICUS RNA POLYMERASE HOLOENZYME AT 4 A RESOLUTION Classification TRANSCRIPTION Compound RNA POLYMERASE, ALPHA SUBUNIT Source ORGANISM_SCIENTIFIC: Thermus aquaticus; Sequence A:  LKAPVFTATTQGDHYGEFVLEPLERGFGVTLGNPLRRILL SSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKEL VVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNP DLHIATLEEGGKLYMEVRVDRGVGYVPAERHGIKDRINAI PVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSV TPLEALNQAVAILKEHLNYFANPE B:  LKAPVFTATTQGDHYGEFVLEPLERGFGVTLGNPLRRILL SSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKEL VVRFLDPKMASTTLILRAEGPKEVRAGDFTPSADVEIMNP DLHIATLEEGGKLYMEVRVDRGVGYVPAERHGIKDRINAI PVDAIFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSV TPLEALNQAVAILKEHLNYF C:  EIKRFGRIREVIPLPPLTEIQVESYKKALQADVPPEKREN VGIQAAFKETFPIEEGLVLDFLEYRIGDPPFSQDECREKD LTYQAPLYARLQLIHKDTGLIKEDEVFLGHLPLMTEDGSF IINGADRVIVSQIHRSPGVYFTPDPARPGRYIASIIPLPK RGPWIDLEVEASGVVTMKVNKRKFPLVLLLRVLGYDQETL VRELSGLLDEAVLAMRPEEAMVRLFTLLRPGLAYLFGLLA DPKRYDLGEAGRYKAEEKLGVGLSGRTLVFKDEVFLPTLR YLFALTAGVPGHEVDDIDHLGNRRIRTVGELMADQFRVGL ARLARGVRERMVMGSPDTLTPAKLVNSRPLEAALREFFSR SQLSQFKDETNPLSSLRHKRRISALGPGGLTRERAGFDVR DVHRTHYGRICPVETPEGANIGLITSLAAYARVDALGFIR TPYRRVKNGVVTEEVVYMTASEEDRYTIAQANTPLEGDRI ATDRVVARRRGEPVIVAPEEVEFMDVSPKQVFSLNTNLIP FLEHDDANRALMGSNMQTQAVPLIRAQAPVVMTGLEERVV RDSLAALYAEEDGEVVKVDGTRIAVRYEDGRLVHPLRRYA RSNQGTAFDQRPRVRVGQRVDLLADGPASEEGFLALGQNV LVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEA RDTKLGPERITRDIPHLSEAALRDLDEEGIVRIGAEVKPG DILVGRTSFKGEQEPSPEERLLRSIFGEKARDVKDTSLRV PPGEGGIVVGRLRLRRGDPGVELKPGVREVVRVFVAQKRK LQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILN PLGVPSRMNLGQILETHLGLAGYFLGQRYISPVFDGATEP EIKELLAEAFNLYFGKRQGEGFGVDKREKEVLARAEKLGL VSPGKSPEEQLKELFDLGKVVLYDGRTGEPFEGPIVVGQM FIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRF GEMEVWALEAYGAAHTLQEMLTIKSDDIEGRNAAYQAIIK GEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIF EGLA D:  KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERD GLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVTR SIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATE LEQVLYFNKYIVLDPKGAVLDGVPVEKRQLLTDEEDARMG AEAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLE VVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFAT SDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEA VDAVIDNGRRGSPVTNPGSERPLRSLTDILSGKQGRFRQN LLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFL LKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHG KVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFN ADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEP LAKPSRDIILGLYYITQVRKEKKGAGMAFATPEEALAAYE RGEVALNAPIVVAGRETSVGRLKFVFANPDEALLAVAHGL LDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQ ELIQMDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYY GFTLSTTSGITIGIDDAVIPEEKQRYLEEADRKLRQIEQA YEMGFLTDRERYDQVIQLWTETTEKVTQAVFKNFEENYPF NPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGETFEVPV RSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRK LVDVAHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKR SDIESGLYGRVLAREVEALGRRLEEGRYLSLEDVHFLIKA AEAGEVREVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSI GEAVGVVAAESIGEPGTQLTMRTPRVIELFEARRPKAKAV ISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLV KDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQ KVYRAQGVKLHDKHIEIVVRQMLKYVEVTDPGDSRLLEGQ VLEKWDVEALNERLIAVPVAWKPLLMGVTKSALSTKSWLS AASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGT GSDFVRFTQVVDQRTLKAIEEAR E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHRFKNTVLE PEERPKMRTLEGLYDDPNAVTWAMKELLTGRLFFGENLVP EDRLQKEMERLY H:  SDPVRQYLHEIGQVPLLTLEEEIDLARKVEEGMEAIKKLS EATGLDQELIREVVRAKILGTARVEEVDGKLKSLPKELKR YLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDL IQEGNQGLIRAVEKFEYKRRFKFSTYATWWIRQAINRAIA DQARTIRIPVHMVETINKLSRTARQLQQELGREPSYEEIA EAMGPGWDAKRVEETLKIAQEPVSLETPIDFIPDENLPSP VEAAAQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREH TLEEVGAYFGVTRERIRQIENKALRKLKYHESRTRKLRDF LE Description Functional site 1) chain D residue 69 type sequence E description BINDING SITE FOR RESIDUE ZN D 2003 source : AC1 2) chain D residue 70 type sequence G description BINDING SITE FOR RESIDUE ZN D 2003 source : AC1 3) chain C residue 836-848 type prosite sequence GDKLANRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKLANrHGNKGV source prosite : PS01166 4) chain H residue 397-423 type prosite sequence TLEEVGAYFGVTRERIRQIENKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGayfgVTrerIrQIEnkaLrkL source prosite : PS00716 5) chain H residue 202-209 type prosite sequence LIEANLRL description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL source prosite : PS00867 6) chain H residue 413-432 type DNA_BIND sequence RQIENKALRKLKYHESRTRK description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 7) chain D residue 1201 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 8) chain D residue 1204 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 9) chain D residue 73 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 10) chain D residue 76 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 11) chain D residue 739 type DNA_BIND sequence D description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 12) chain D residue 741 type DNA_BIND sequence D description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 13) chain D residue 743 type DNA_BIND sequence D description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 14) chain D residue 1112 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 15) chain D residue 1194 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1

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