eF-site ID 6n60-ABCDEFM PDB Code 6n60 Chain A, B, C, D, E, F, M Title Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA and Microcin J25 (MccJ25) Classification TRANSFERASE/DNA Compound DNA-directed RNA polymerase subunit alpha Source (6N60) Sequence A:  VTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALR RILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLN LKGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIV KPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEED ERPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIE METNGTIDPEEAIRRAATILAEQLEAFVDLE B:  TEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRR ILLSSMPGCAVTEVEIDGVEYSTKEGVQEDILEILLNLKG LAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVKPQ HVICHLTDENASISMRIKVQRGRGYVPASTRLLVDACYSP VERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRR AATILAEQLEAFVDLEVL C:  YSYTEKKRIRKDFGKRPQVLDVPYLLSIQLDSFQKFIEQD PEGQYGLEAAFRSVFPIQSYSGNSELQYVSYRLGEPVFDV QECQIRGVTYSAPLRVKLRLVIYERGTVKDIKEQEVYMGE IPLMTDNGTFVINGTERVIVSQLHRSPGVFFDSDKGKTHS SGKVLYNARIIPYRGSWLDFEFDPKDNLFVRIDRRRKLPA TIILRALNYTTEQILDLFFEKVIFEIRDNKLQMELVPERL RGETASFDIEANGKVYVEKGRRITARHIRQLEKDDVKLIE VPVEYIAGKVVAKDYIDESTGELICAANMELSLDLLAKLS QSGHKRIETLFTNDLDHGPYISETLRVDPTNDRLSALVEI YRMMRPGEPPTREAAESLFENLFFSEDRYDLSAVGRMKFN RSLLREEIEGSGILSKDDIIDVMKKLIDIRNGKGEVDDID HLGNRRIRSVGEMAENQFRVGLVRVERAVKERLSLGDLDT LMPQDMINAKPISAAVKEFFGSSQLSQFMDQNNPLSEITH KRRISALGPGGLTRERAGFEVRDVHPTHYGRVCPIETPEG PNIGLINSLSVYAQTNEYGFLETPYRKVTDGVVTDEIHYL SAIEEGNYVIAQANSNLDEEGHFVEDLVTCRSKGESSLFS RDQVDYMDVSTQQVVSVGASLIPFLEHDDANRALMGANMQ RQAVPTLRADKPLVGTGMERAVAVDSGVTAVAKRGGVVQY VDASRIVIKVNEDEMYPGEAGIDIYNLTKYTRSNQNTCIN QMPCVSLGEPVERGDVLADGPSTDLGELALGQNMRVAFMP WNGYNFEDSILVSERVVQEDRFTTIHIQELACVSRDTKLG PEEITADIPNVGEAALSKLDESGIVYIGAEVTGGDILVGK VTPKGETQLTPEEKLLRAIFGEKASDVKDSSLRVPNGVSG TVIDVQVFTRDGVEKDKRALEIEEMQLKQAKKDLSEELQI LEAGLFSRIRAVLVAGGVEAEKLDKLPRDRWLELGLTDEE KQNQLEQLAEQYDELKHEFEKKLEAKRRKITQGDDLAPGV LKIVKVYLAVKRRIQPGDKMAGRHGNKGVISKINPIEDMP YDENGTPVDIVLNPLGVPSRMNIGQILETHLGMAAKGIGD KINAMLKQQQEVAKLREFIQRAYDLGADVRQKVDLSTFSD EEVMRLAENLRKGMPIATPVFDGAKEAEIKELLKLGDLPT SGQIRLYDGRTGEQFERPVTVGYMYMLKLNHLVDDKMHAR STGSYSLVTQQPLGGAQFGGQRFGEMEVWALEAYGAAYTL QEMLTVKSDDVNGRTKMYKNIVDGNHQMEPGMPESFNVLL KEIRSLGINIELEDE D:  EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDG LFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQT KVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRDI ERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGDE FDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKRK KLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPL DGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNE KRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ GRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALE LFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCA AYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAN GEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAER LYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVG RAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLK PTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIIS EAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSK AMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAA QIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFIS THGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG THEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTAD ILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVC AHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRTF HISSIQVKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLI DEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTG GLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLV ITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGPEA PHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIEVI VRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANG KVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAA VAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRR E:  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPE ENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL F:  TTDPVRMYMREMGTVELLTREGEIDIAKRIEDGINQVQCS VAEYPEAITYLPKQFDYVNSMTIEQVKDINRRMSIGEAKA RRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGL MKAVDKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRI PVHMIETINKLNRISRQMLQEMGREPTPEELAERMLMPED KIRKVLKIAKEPISMETPIGDDEDSHLGDFIEDTTLELPL DSATTESLRAATHDVLAGLTAREAKVLRMRFGIDMNTDYT LEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSF M:  GGAGHVPEYFVGIGTPISFYG 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 816 type sequence T description binding site for residue ZN D 1503 source : AC3 10) chain D residue 883 type sequence R description binding site for residue ZN D 1503 source : AC3 11) chain D residue 888 type sequence C description binding site for residue ZN D 1503 source : AC3 12) chain D residue 895 type sequence C description binding site for residue ZN D 1503 source : AC3 13) chain D residue 898 type sequence C description binding site for residue ZN D 1503 source : AC3 14) chain M residue 4 type SITE sequence G description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 15) chain D residue 895 type SITE sequence C description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 16) chain D residue 898 type SITE sequence C description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 17) chain M residue 7 type SITE sequence P description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 18) chain M residue 10 type SITE sequence F description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 19) chain M residue 19 type SITE sequence F description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 20) chain M residue 20 type SITE sequence Y description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 21) chain D residue 462 type SITE sequence D description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 22) chain D residue 464 type SITE sequence D description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 23) chain D residue 814 type SITE sequence C description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 24) chain D residue 888 type SITE sequence C description Essential for permeation into bacteria => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI1 25) chain M residue 9 type SITE sequence Y description Essential for permeation into bacteria and for RNAP inhibition => ECO:0000269|PubMed:18632663 source Swiss-Prot : SWS_FT_FI2 26) chain M residue 1 type CROSSLNK sequence G description Isoglutamyl glycine isopeptide (Gly-Glu) => ECO:0000269|PubMed:14531661, ECO:0000269|PubMed:14531690, ECO:0000269|PubMed:14531691 source Swiss-Prot : SWS_FT_FI3 27) chain M residue 8 type CROSSLNK sequence E description Isoglutamyl glycine isopeptide (Gly-Glu) => ECO:0000269|PubMed:14531661, ECO:0000269|PubMed:14531690, ECO:0000269|PubMed:14531691 source Swiss-Prot : SWS_FT_FI3 28) chain C residue 1063-1075 type prosite sequence GDKMAGRHGNKGV description RNA_POL_BETA RNA polymerases beta chain signature. GdKMAGrHGNKGV source prosite : PS01166 29) chain F residue 403-416 type prosite sequence DLIQEGNIGLMKAV description SIGMA70_1 Sigma-70 factors family signature 1. DLIQeGnIGLMkAV source prosite : PS00715 30) chain F residue 572-598 type prosite sequence TLEEVGKQFDVTRERIRQIEAKALRKL description SIGMA70_2 Sigma-70 factors family signature 2. TleEVGkqfdVTrerIrQIEakaLrkL source prosite : PS00716

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