X-ray crystal structure of a bacterial reiterative transcription complex of pyrG promoter

X-ray crystal structure of a reiterative transcription complex reveals an atypical RNA extension pathway.

Residue D ALA 96 and Residue D THR 97 that are next to each other in the sample sequence are not properly linked: distance between C and N is 1.20.

DNA-directed RNA polymerase subunit alpha

DNA-directed RNA polymerase subunit beta

DNA-directed RNA polymerase subunit beta'

DNA-directed RNA polymerase subunit omega

DNA (5'-D(P*GP*GP*TP*GP*CP*AP*TP*CP*AP*GP*AP*GP*CP*CP*CP*AP*AP*AP*A)-3')

DNA (5'-D(*TP*AP*TP*AP*AP*TP*GP*GP*GP*CP*TP*GP*AP*TP*GP*CP*AP*CP*C)-3')

RNAP subunit alpha,RNA polymerase subunit alpha,Transcriptase subunit alpha

RNAP subunit beta,RNA polymerase subunit beta,Transcriptase subunit beta

RNAP subunit beta',RNA polymerase subunit beta',Transcriptase subunit beta'

RNAP omega subunit,RNA polymerase omega subunit,Transcriptase subunit omega

MLDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIIL
NLKELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKD
RINAIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQAAAVAAPEEAK
EPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEKKGFTLKE

MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRENVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQ
DECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIA
SIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVLGYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFT
LLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEKLGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGH
EVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERMLMGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNP
LSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICPVETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVT
DEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGEPVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALM
GSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEEDGEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQR
PRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFDGYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE
RITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTSFKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIV
VRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLANRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRM
NLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE
EQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHMVEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWAL
EAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPSVPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASKR

MKKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEV
TKSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYRE
LRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGE
ILAELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAA
QVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARV
YPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEE
MKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQ
GAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLH
QCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVL
VEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKK
GAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRI
LFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEK
KQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCG
LRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISV
PLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGV
CQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAVISEIDGV
VRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQG
VKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASF
QNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEAKERPAARRGVKREQP
GKQA

MAEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLEPEERPKMQTLEGLFDDPNAVTWAMKELLTGRLVFGENLV
PEDRLQKEMERLYPVEREE

MKKSKRKNAQAQEAQETEVLVQEEAEELPEFPEGEPDPDLEDPDLTLEDDLLDLPEEGEGLDLEEEEEDLPIPKISTSDP
VRQYLHEIGQVPLLTLEEEVELARKVEEGMEAIKKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDPKTVEEID
QKLKSLPKEHKRYLHIAREGEAARQHLIEANLRLVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRFKFSTYAT
WWIRQAINRAIADQARTIRIPVHMVETINKLSRTARQLQQELGREPTYEEIAEAMGPGWDAKRVEETLKIAQEPVSLETP
IGDEKDSFYGDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVLKLRKGLIDGREHTLEEVGAFFGVTRERIRQI
ENKALRKLKYHESRTRKLRDFLD

(DC)(DC)(DT)(DG)(DC)(DA)(DT)(DC)(DA)(DG)(DA)(DG)(DC)(DC)(DC)(DA)(DA)(DA)(DA)(DT)
(DA)(DC)

(DT)(DA)(DT)(DA)(DA)(DT)(DG)(DG)(DG)(DA)(DG)(DC)(DT)(DG)(DG)(DC)(DT)(DC)(DT)(DG)
(DA)(DT)(DG)(DC)(DA)(DG)(DG)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)

National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Thermus thermophilus, RNA polymerase, reiterative transcription, holoenzyme, transcription-DNA-RNA complex
binding site for Di-nucleotide GTP I 1 and G I 2