eF-site ID 5x21-ABCDEF PDB Code 5x21 Chain A, B, C, D, E, F Title Crystal structure of Thermus thermophilus transcription initiation complex with GpA and pseudouridimycin (PUM) Classification TRANSFERASE/DNA Compound DNA-directed RNA polymerase subunit alpha Source ORGANISM_SCIENTIFIC: Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579); 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 FQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEE GRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQ KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFH TGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGVVR IEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAG QPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVK LHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEA LNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQN TTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVR FTQVVDQKTLKAIEEA E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE PEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLVP EDRLQKEMERLYPV F:  SDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLS EITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVE EIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVS IAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFST YATWWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQ LQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSL ETPIGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKA LSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERI RQIENKALRKLKYHESRTRKLRDFLD Description Functional site 1) chain A residue 51 type sequence T description binding site for residue MG A 2001 source : AC1 2) chain A residue 170 type sequence V description binding site for residue MG A 2001 source : AC1 3) chain A residue 171 type sequence F description binding site for residue MG A 2001 source : AC1 4) chain A residue 172 type sequence S description binding site for residue MG A 2001 source : AC1 5) chain A residue 175 type sequence R description binding site for residue MG A 2001 source : AC1 6) chain C residue 387 type sequence S description binding site for residue MG C 2000 source : AC2 7) chain C residue 389 type sequence S description binding site for residue MG C 2000 source : AC2 8) chain C residue 392 type sequence S description binding site for residue MG C 2000 source : AC2 9) chain B residue 154 type sequence E description binding site for residue MG D 1601 source : AC3 10) chain B residue 168 type sequence D description binding site for residue MG D 1601 source : AC3 11) chain D residue 840 type sequence K description binding site for residue MG D 1601 source : AC3 12) chain D residue 1112 type sequence C description binding site for residue ZN D 1602 source : AC4 13) chain D residue 1194 type sequence C description binding site for residue ZN D 1602 source : AC4 14) chain D residue 1201 type sequence C description binding site for residue ZN D 1602 source : AC4 15) chain D residue 1204 type sequence C description binding site for residue ZN D 1602 source : AC4 16) chain D residue 58 type sequence C description binding site for residue ZN D 1603 source : AC5 17) chain D residue 60 type sequence C description binding site for residue ZN D 1603 source : AC5 18) chain D residue 62 type sequence K description binding site for residue ZN D 1603 source : AC5 19) chain D residue 73 type sequence C description binding site for residue ZN D 1603 source : AC5 20) chain D residue 76 type sequence C description binding site for residue ZN D 1603 source : AC5 21) chain D residue 739 type sequence D description binding site for residue MG D 1604 source : AC6 22) chain D residue 741 type sequence D description binding site for residue MG D 1604 source : AC6 23) chain D residue 743 type sequence D description binding site for residue MG D 1604 source : AC6 24) chain F residue 292 type sequence A description binding site for residue MG F 2001 source : AC7 25) chain F residue 296 type sequence G description binding site for residue MG F 2001 source : AC7 26) chain F residue 299 type sequence W description binding site for residue MG F 2001 source : AC7 27) chain C residue 445 type sequence E description binding site for residue PUM I 101 source : AC9 28) chain C residue 846 type sequence K description binding site for residue PUM I 101 source : AC9 29) chain D residue 704 type sequence R description binding site for residue PUM I 101 source : AC9 30) chain D residue 706 type sequence P description binding site for residue PUM I 101 source : AC9 31) chain D residue 737 type sequence N description binding site for residue PUM I 101 source : AC9 32) chain D residue 1084 type sequence T description binding site for residue PUM I 101 source : AC9 33) chain D residue 1235 type sequence Q description binding site for residue PUM I 101 source : AC9 34) chain D residue 1238 type sequence M description binding site for residue PUM I 101 source : AC9 35) chain D residue 1241 type sequence F description binding site for residue PUM I 101 source : AC9 36) chain F residue 383-402 type DNA_BIND sequence LEEVGAFFGVTRERIRQIEN description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 37) 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 38) 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 39) chain D residue 60 type DNA_BIND sequence C description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 40) 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 41) 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 42) 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 43) 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 44) 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 45) 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 46) 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 47) chain F residue 382-408 type prosite sequence TLEEVGAFFGVTRERIRQIENKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGaffgVTrerIrQIEnkaLrkL source prosite : PS00716 48) chain F residue 187-194 type prosite sequence LIEANLRL description CPSASE_2 Carbamoyl-phosphate synthase subdomain signature 2. LIEANLRL source prosite : PS00867 49) 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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