eF-site ID 4ljz-ABCDEFGHIJKL PDB Code 4ljz Chain A, B, C, D, E, F, G, H, I, J, K, L Title Crystal Structure Analysis of the E.coli holoenzyme Classification TRANSFERASE Compound DNA-directed RNA polymerase subunit alpha Source Escherichia coli (strain ATCC 33849 / DSM 4235 / NCIB 12045 / K12 / DH1) (RPOD_ECOLI) Sequence A:  FLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRIL LSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKG LAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQ HVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERP IGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMET NGTIDPEEAIRRAATILAEQLEAF B:  TEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRR ILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVK PQHVICHLTDENASISMRIKVQRGRGYVPASTRIHLVDAC YSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEA IRRAATILAEQLEAFVDLEV C:  YSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDV QECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEV YMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKG KTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRR KLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELV PERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDV KLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLL AKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSA LVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGR MKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEV DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLG DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLS EITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIE TPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGES SLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMG ANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG VVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQN TCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRV AFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRD TKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDI LVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPN GVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSE ELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGL TDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDL APGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPI EDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAK GIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLS TFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLG DLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDK MHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG AAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPES FNVLLKEIRSLGINIELEDE D:  LKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYR TFKPERDGLFCARIFGPVKDYECLCGKYKRLKHRGVICEK CGVEVTQTKVRRERMGHIELASPTAHIWFLKSLPSRIGLL LDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQYLD ALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNE TNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPP DLRPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAA PDIIVRNEKRMLQEAVDALLDNGRRGRAITGSNKRPLKSL ADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCG LPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAV VWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAI QLHPLVCAAYNADFDGDQMAVHVPLTLEAQLEARALMMST NNILSPANGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVL TGPKEAERLYRSGLASLHARVKVRITEYEKDANGELVAKT SLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNT CYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIP EKKHEIISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWA AANDRVSKAMMDNLQTETVINRDGQEEKQVSFNSIYMMAD SGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFREGL NVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDL VVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAED VLKPGTADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVS CDTDFGVCAHCYGRDLARGHIINKGEAIGVIAAQSIGEPG TQLTTGGLPRVADLFEARRPKEPAILAEISGIVSFGKETK GKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVI SDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKIND KHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANR ELEANGKVGATYSRDLLGITKASLATESFISAASFQETTR VLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRM RRRAAG E:  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPE ENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQ AVTAIAEGR F:  GRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQ CSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDDPEL AREKFAELRAQYVVTRDTIKATAQEEILKLSEVFKQFRLV PKQFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNF ITLFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQ KLQQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEA NLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYR RGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINK LNRISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAK EPISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRA ATHDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDV TRERIRQIEAKALRKLRHPSRSEVLRSFLD G:  FLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRRIL LSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKG LAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQ HVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERP IGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEMET NGTIDPEEAIRRAATILAEQLEAFVDLE H:  TEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRR ILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVK PQHVICHLTDENASISMRIKVQRGRGYVPASTRLLVDACY SPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAI RRAATILAEQLEAFVDL I:  YSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDV QECQIRGVTYSAPLRVKLRLVIYEREAPEGTVKDIKEQEV YMGEIPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKG KTHSSGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRR KLPATIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELV PERLRGETASFDIEANGKVYVEKGRRITARHIRQLEKDDV KLIEVPVEYIAGKVVAKDYIDESTGELICAANMELSLDLL AKLSQSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSA LVEIYRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGR MKFNRSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEV DDIDHLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLG DLDTLMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLS EITHKRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIE TPEGPNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDE IHYLSAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGES SLFSRDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMG ANMQRQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGG VVQYVDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQN TCINQMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRV AFMPWNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRD TKLGPEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDI LVGKVTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPN GVSGTVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSE ELQILEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGL TDEEKQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDL APGVLKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPI EDMPYDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAK GIGDKINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLS TFSDEEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLG DLPTSGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDK MHARSTGSYSLVTQQPLGGKAQFGGQRFGEMEVWALEAYG AAYTLQEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPES FNVLLKEIRSLGINIELEDE J:  EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDG LFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQT KVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDI ERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDE FDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPL DGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNE KRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGLG KRVDYSGRSVITVGPYLRLHQCGLPKKMALELFKPFIYGK LELRGLATTIKAAKKMVEREEAVVWDILDEVIREHPVLLN RAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGD QMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQ DVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASL HARVKVRITEYEKDANGELVAKTSLKDTTVGRAILWMIVP KGLPYSIVNQALGKKAISKMLNTCYRILGLKPTVIFADQI MYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEI QEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTE TVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMR GLMAKPDGSIIETPITANFREGLNVLQYFISTHGARKGLA DTALKTANSGYLTRRLVDVAQDLVVTEDDCGTHEGIMMTP VIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLL HEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLA RGHIINKGEAIGVIAAQSIGEPGTQLTSSIQVKNKGSIKL SNVKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYG AVLAKGDGEQVAGGETVANWDPHTMPVITEVSGFVRFTDM IDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRPALKI VDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDT LARIPQGLPRVADLFEARRPKEPAILAEISGIVSFGKETK GKRRLVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVI SDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKIND KHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANR ELEANGKVGATYSRDLLGITKASLATESFISAASFQETTR VLTEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRM RRRAA K:  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPE ENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL L:  TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCS VAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDDPELAR EKFAELRAQYVVTRDTIKATAQEEILKLSEVFKQFRLVPK QFDYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFIT LFTGNETSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKL QQIEEETGLTIEQVKDINRRMSIGEAKARRAKKEMVEANL RLVISIAKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRG YKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLN RISRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEP ISMETPIGDDEDSHLGDFIEDTTLELPLDSATTESLRAAT HDVLAGLTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTR ERIRQIEAKALRKLRHPSRSEVLRSFLDD Description Functional site 1) chain D residue 460 type sequence D description BINDING SITE FOR RESIDUE MG D 1501 source : AC1 2) chain D residue 462 type sequence D description BINDING SITE FOR RESIDUE MG D 1501 source : AC1 3) chain D residue 464 type sequence D description BINDING SITE FOR RESIDUE MG D 1501 source : AC1 4) chain D residue 70 type sequence C description BINDING SITE FOR RESIDUE ZN D 1502 source : AC2 5) chain D residue 72 type sequence C description BINDING SITE FOR RESIDUE ZN D 1502 source : AC2 6) chain D residue 85 type sequence C description BINDING SITE FOR RESIDUE ZN D 1502 source : AC2 7) chain D residue 88 type sequence C description BINDING SITE FOR RESIDUE ZN D 1502 source : AC2 8) chain D residue 814 type sequence C description BINDING SITE FOR RESIDUE ZN D 1503 source : AC3 9) chain D residue 888 type sequence C description BINDING SITE FOR RESIDUE ZN D 1503 source : AC3 10) chain D residue 895 type sequence C description BINDING SITE FOR RESIDUE ZN D 1503 source : AC3 11) chain D residue 898 type sequence C description BINDING SITE FOR RESIDUE ZN D 1503 source : AC3 12) chain J residue 460 type sequence D description BINDING SITE FOR RESIDUE MG J 1501 source : AC4 13) chain J residue 462 type sequence D description BINDING SITE FOR RESIDUE MG J 1501 source : AC4 14) chain J residue 464 type sequence D description BINDING SITE FOR RESIDUE MG J 1501 source : AC4 15) chain J residue 70 type sequence C description BINDING SITE FOR RESIDUE ZN J 1502 source : AC5 16) chain J residue 72 type sequence C description BINDING SITE FOR RESIDUE ZN J 1502 source : AC5 17) chain J residue 85 type sequence C description BINDING SITE FOR RESIDUE ZN J 1502 source : AC5 18) chain J residue 88 type sequence C description BINDING SITE FOR RESIDUE ZN J 1502 source : AC5 19) chain J residue 814 type sequence C description BINDING SITE FOR RESIDUE ZN J 1503 source : AC6 20) chain J residue 888 type sequence C description BINDING SITE FOR RESIDUE ZN J 1503 source : AC6 21) chain J residue 895 type sequence C description BINDING SITE FOR RESIDUE ZN J 1503 source : AC6 22) chain J residue 898 type sequence C description BINDING SITE FOR RESIDUE ZN J 1503 source : AC6 23) chain F residue 403-416 type prosite sequence DLIQEGNIGLMKAV description SIGMA70_1 Sigma-70 factors family signature 1. DLIQeGnIGLMkAV source prosite : PS00715 24) chain F residue 572-598 type prosite sequence TLEEVGKQFDVTRERIRQIEAKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGkqfdVTrerIrQIEakaLrkL source prosite : PS00716 25) chain C residue 1063-1075 type prosite sequence GDKMAGRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKMAGrHGNKGV source prosite : PS01166 26) chain F residue 573-592 type DNA_BIND sequence LEEVGKQFDVTRERIRQIEA description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 27) chain L residue 573-592 type DNA_BIND sequence LEEVGKQFDVTRERIRQIEA description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963 source Swiss-Prot : SWS_FT_FI1 28) chain F residue 562 type SITE sequence R description Interaction with anti-sigma factors source Swiss-Prot : SWS_FT_FI2 29) chain L residue 562 type SITE sequence R description Interaction with anti-sigma factors source Swiss-Prot : SWS_FT_FI2

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