eF-site ID 3wod-ABCDEFGH PDB Code 3wod Chain A, B, C, D, E, F, G, H click to enlarge Title RNA polymerase-gp39 complex Classification TRANSFERASE/TRANSCRIPTION Compound DNA-directed RNA polymerase subunit alpha Source ORGANISM_SCIENTIFIC: Thermus thermophilus; Sequence A:  LKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILL SSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKEL VVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIMNP DLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRINAI PVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSV TPLEALNQAVEILREHLTYFSNPQA B:  SKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRI LLSSIPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLK ELVVRFLNPSLQTVTLLLKAEGPKEVKARDFLPVADVEIM NPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIKDRIN AIPVDAVFSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDG SVTPLEALNQAVEILREHLTYFSNPQAAAVAA C:  MEIKRFGRIREVIPLPPLTEIQVESYRRALQADVPPEKRE NVGIQAAFRETFPIEEEDKGKGGLVLDFLEYRLGEPPFPQ DECREKDLTYQAPLYARLQLIHKDTGLIKEDEVFLGHIPL MTEDGSFIINGADRVIVSQIHRSPGVYFTPDPARPGRYIA SIIPLPKRGPWIDLEVEPNGVVSMKVNKRKFPLVLLLRVL GYDQETLARELGAYGELVQGLMDESVFAMRPEEALIRLFT LLRPGDPPKRDKAVAYVYGLIADPRRYDLGEAGRYKAEEK LGIRLSGRTLARFEDGEFKDEVFLPTLRYLFALTAGVPGH EVDDIDHLGNRRIRTVGELMTDQFRVGLARLARGVRERML MGSEDSLTPAKLVNSRPLEAAIREFFSRSQLSQFKDETNP LSSLRHKRRISALGPGGLTRERAGFDVRDVHRTHYGRICP VETPEGANIGLITSLAAYARVDELGFIRTPYRRVVGGVVT DEVVYMTATEEDRYTIAQANTPLEGNRIAAERVVARRKGE PVIVSPEEVEFMDVSPKQVFSVNTNLIPFLEHDDANRALM GSNMQTQAVPLIRAQAPVVMTGLEERVVRDSLAALYAEED GEVAKVDGNRIVVRYEDGRLVEYPLRRFYRSNQGTALDQR PRVVVGQRVRKGDLLADGPASENGFLALGQNVLVAIMPFD GYNFEDAIVISEELLKRDFYTSIHIERYEIEARDTKLGPE RITRDIPHLSEAALRDLDEEGVVRIGAEVKPGDILVGRTS FKGESEPTPEERLLRSIFGEKARDVKDTSLRVPPGEGGIV VRTVRLRRGDPGVELKPGVREVVRVYVAQKRKLQVGDKLA NRHGNKGVVAKILPVEDMPHLPDGTPVDVILNPLGVPSRM NLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQ AFEVYFGKRKGEGFGVDKREVEVLRRAEKLGLVTPGKTPE EQLKELFLQGKVVLYDGRTGEPIEGPIVVGQMFIMKLYHM VEDKMHARSTGPYSLITQQPLGGKAQFGGQRFGEMEVWAL EAYGAAHTLQEMLTLKSDDIEGRNAAYEAIIKGEDVPEPS VPESFRVLVKELQALALDVQTLDEKDNPVDIFEGLASK D:  KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPER DGLFDERIFGPIKDYECACGKYKRQRFEGKVCERCGVEVT KSIVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSAT ELEQVLYFSKYIVLDPKGAILNGVPVEKRQLLTDEEYREL RYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG VALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEI LAELPEPYLFRAEEEGVVELKELEEGAFLVLRREDEPVAT YFLPVGMTPLVVHGEIVEKGQPLAEAKGLLRMPRQVRAAQ VEAEEEGETVYLTLFLEWTEPKDYRVQPHMNVVVPEGARV EAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVY PFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVR NVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEM KHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLP PDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQG APEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLR SLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQ CGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQR DIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLV EGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARI QMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKG AGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKY VFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRIL FARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLR LGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKK QYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTE KVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGL RGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGG ADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVP LFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLE EGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVC QKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMGLP RVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESE GFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLE AKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMK YVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAW KPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKD ELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEE ARKEAVEA E:  AEPGIDKLFGMVDSKYRLTVVVAKRAQQLLRHGFKNTVLE PEERPKMQTLEGLFDDPNAETWAMKELLTGRLVFGENLVP EDRLQKEMERIYPGE F:  KISTSDPVRQYLHEIGQVPLLTLEEEVELARKVEEGMEAI KKLSEITGLDPDLIREVVRAKILGSARVRHIPGLKETLDP KTVEEIDQKLKSLPKEHKRYLHIAREGEAARQHLIEANLR LVVSIAKKYTGRGLSFLDLIQEGNQGLIRAVEKFEYKRRF KFSTYATWWIRQAINRAIADQAQEPVSLETPIGDEKDSFY GDFIPDEHLPSPVDAATQSLLSEELEKALSKLSEREAMVL KLRKGLIDGEEVGAFFGVTRERIRQIENKALRKLKYHE G:  GFVEPYIRLFEAIPDAETELATFYDADLDTLPPRMFLPSG DLYTPPGPVRLEEIKRKRRVRLVKVSIYRFEHVGLGLAAR PYAYAYAWQGDNGILHLYHAPVVLEDEVTYNESYVRLMRA MGHVDAF H:  FVEPYIRLFEAIPDAETELATFYDADLDTLPPRMFLPSGD LYTPPGPVRLEEIKRKRRVRLVKVSIYRYAYAYAWQGDNG ILHLYHAPVVL Description Functional site 1) chain D residue 1112 type sequence C description BINDING SITE FOR RESIDUE ZN D 1601 source : AC1 2) chain D residue 1194 type sequence C description BINDING SITE FOR RESIDUE ZN D 1601 source : AC1 3) chain D residue 1195 type sequence Q description BINDING SITE FOR RESIDUE ZN D 1601 source : AC1 4) chain D residue 1201 type sequence C description BINDING SITE FOR RESIDUE ZN D 1601 source : AC1 5) chain D residue 1204 type sequence C description BINDING SITE FOR RESIDUE ZN D 1601 source : AC1 6) chain D residue 58 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 7) chain D residue 1201 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 8) chain D residue 1204 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 9) chain D residue 60 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 10) chain D residue 73 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 11) chain D residue 76 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 12) chain D residue 739 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 13) chain D residue 741 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 14) chain D residue 743 type BINDING sequence D description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 15) chain D residue 1112 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 16) chain D residue 1194 type BINDING sequence C description BINDING => ECO:0000255|HAMAP-Rule:MF_01322 source Swiss-Prot : SWS_FT_FI1 17) chain C residue 836-848 type prosite sequence GDKLANRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKLANrHGNKGV source prosite : PS01166 18) 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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