eF-site ID 5ipn-ABCDEF
PDB Code 5ipn
Chain A, B, C, D, E, F
Title SigmaS-transcription initiation complex with 4-nt nascent RNA
Classification TRANSCRIPTION, TRANSFERASE/DNA/RNA
Compound DNA-directed RNA polymerase subunit alpha
Source Escherichia coli (strain K12) (5IPN)
Sequence A:  TEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRR
ILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL
KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVK
PQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDE
RPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEM
ETNGTIDPEEAIRRAATILAEQLEAFVDLR
B:  TEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRR
ILLSSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNL
KGLAVRVQGKDEVILTLNKSGIGPVTAADITHDGDVEIVK
PQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDE
RPIGRLLVDACYSPVERIAYNVEAARVEQRTDLDKLVIEM
ETNGTIDPEEAIRRAATILAEQLEAFVD
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:  EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERD
GLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQ
TKVRRERMGHIELASPTAHIWFLKSLPSRIGLLLDMPLRD
IERVLYFESYVVIEGGMTNLERQQILTEEQYLDALEEFGD
EFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKR
KKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVP
LDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRN
EKRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGK
QGRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMAL
ELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE
VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVC
AAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPA
NGEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAE
RLYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTV
GRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGL
KPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEII
SEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVS
KAMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSA
AQIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFI
STHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDC
GTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTA
DILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGV
CAHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTMRT
FHIGGAASRAAAESSIQVKNKGSIKLSNVKSVVNSSGKLV
ITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGG
ETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELT
GLSSLVVLDSAERTAGGKDLRPALKIVDAQGNDVLIPGTD
MPAQYFLPGKAIVQLEDGVQISSGDTLARIPQESGGTKDI
TGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRR
LVITPVDGSDPYEEMIPKWRQLNVFEGERVERGDVISDGP
EAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIE
VIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEA
NGKVGATYSRDLLGITKASLATESFISAASFQETTRVLTE
AAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRA
AG
E:  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPE
ENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL
F:  RVLDATQLYLGEIGYSPLLTAEEEVYFARRALRGDVASRR
RMIESNLRLVVKIARRYGNRGLALLDLIEEGNLGLIRAVE
KFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPIHIV
KELNVYLRTARELSHKLDHEPSAEEIAEQLDKPVDDVSRM
LRLNERITSVDTPLGGDSEKALLDILADEKENGPEDTTQD
DDMKQSIVKWLFELNAKQREVLARRFGLLGYEAATLEDVG
REIGLTRERVRQIQVEGLRRLREILQTQGLNIEALFL
Description (1)  DNA-directed RNA polymerase subunit alpha, DNA-directed RNA polymerase subunit beta, DNA-directed RNA polymerase subunit beta', DNA-directed RNA polymerase subunit omega, RNA polymerase sigma factor RpoS/DNA Complex


Functional site

1) chain D
residue 70
type
sequence C
description binding site for residue ZN D 1501
source : AC1

2) chain D
residue 72
type
sequence C
description binding site for residue ZN D 1501
source : AC1

3) chain D
residue 85
type
sequence C
description binding site for residue ZN D 1501
source : AC1

4) chain D
residue 88
type
sequence C
description binding site for residue ZN D 1501
source : AC1

5) chain D
residue 814
type
sequence C
description binding site for residue ZN D 1502
source : AC2

6) chain D
residue 888
type
sequence C
description binding site for residue ZN D 1502
source : AC2

7) chain D
residue 895
type
sequence C
description binding site for residue ZN D 1502
source : AC2

8) chain D
residue 898
type
sequence C
description binding site for residue ZN D 1502
source : AC2

9) chain D
residue 460
type
sequence D
description binding site for residue MG D 1503
source : AC3

10) chain D
residue 462
type
sequence D
description binding site for residue MG D 1503
source : AC3

11) chain D
residue 464
type
sequence D
description binding site for residue MG D 1503
source : AC3

12) chain D
residue 983
type MOD_RES
sequence K
description N6-acetyllysine => ECO:0000255|HAMAP-Rule:MF_01322, ECO:0000269|PubMed:18723842
source Swiss-Prot : SWS_FT_FI2

13) chain F
residue 288-307
type DNA_BIND
sequence LEDVGREIGLTRERVRQIQV
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

14) chain D
residue 895
type DNA_BIND
sequence C
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

15) chain D
residue 898
type DNA_BIND
sequence C
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

16) chain D
residue 72
type DNA_BIND
sequence C
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

17) chain D
residue 85
type DNA_BIND
sequence C
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

18) chain D
residue 88
type DNA_BIND
sequence C
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

19) chain D
residue 460
type DNA_BIND
sequence D
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

20) chain D
residue 462
type DNA_BIND
sequence D
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

21) chain D
residue 464
type DNA_BIND
sequence D
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

22) chain D
residue 814
type DNA_BIND
sequence C
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

23) chain D
residue 888
type DNA_BIND
sequence C
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00959
source Swiss-Prot : SWS_FT_FI1

24) chain C
residue 1063-1075
type prosite
sequence GDKMAGRHGNKGV
description RNA_POL_BETA RNA polymerases beta chain signature. GdKMAGrHGNKGV
source prosite : PS01166

25) chain F
residue 118-131
type prosite
sequence DLIEEGNLGLIRAV
description SIGMA70_1 Sigma-70 factors family signature 1. DLIEeGnLGLIrAV
source prosite : PS00715

26) chain F
residue 287-313
type prosite
sequence TLEDVGREIGLTRERVRQIQVEGLRRL
description SIGMA70_2 Sigma-70 factors family signature 2. TleDVGreigLTrerVrQIQvegLrrL
source prosite : PS00716


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