eF-site ID 4lk1-ABCDEFGHIJKL
PDB Code 4lk1
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:  PQSQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDI
IQMINDMGIQVMNTADEDAAEAAAQVLSSVESGRTTDPVR
MYMREMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPE
AITYLLEQYDRVEAEEARLSDLITGFVDDPELAREKFAEL
RAQYVVTRDTIKATAQEEILKLSEVFKQFRLVPKQFDYLV
NSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNE
TSDTWFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEE
TGLTIEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISI
AKKYTNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTY
ATWWIRQAITRSIADQARTIRIPVHMIETINKLNRISRQM
LQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETP
IGDDEDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAG
LTAREAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQI
EAKALRKLRHPSRSEVLRSFLD
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
KRMLQEAVDALLDNGRRGRAITGSNKRPLKSLADMIKGKQ
GRFRQNLLGKRVDYSGRSVITVGPYLRLHQCGLPKKMALE
LFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDEV
IREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCA
AYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPAN
GEPIIVPSQDVVLGLYYMTRDCVNAKGEGMVLTGPKEAER
LYRSGLASLHARVKVRITEYEKDANGELVAKTSLKDTTVG
RAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGLK
PTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIIS
EAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSK
AMMDNLQTETVINRDGQEEKQVSFNSIYMMADSGARGSAA
QIRQLAGMRGLMAKPDGSIIETPITANFREGLNVLQYFIS
THGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDCG
THEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTAD
ILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVC
AHCYGRDLARGHIINKGEAIGVIAAQSIGEPGTQLTSSIQ
VKNKGSIKLSNVKSVVNSSGKLVITSRNTELKLIDEFGRT
KESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMPVITEV
SGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGG
KDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLED
GVQISSGDTLARIPQGLPRVADLFEARRPKEPAILAEISG
IVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQLNVFEG
ERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVY
RLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVE
YSRVKIANRELEANGKVGATYSRDLLGITKASLATESFIS
AASFQETTRVLTEAAVAGKRDELRGLKENVIVGRLIPAGT
GYAYHQDRMRRRAA
K:  ARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPE
ENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAEL
L:  SQLKLLVTRGKEQGYLTYAEVNDHLPEDIVDSDQIEDIIQ
MINDMGIQVMNTADEDAAEAAAQVLSSVESTTDPVRMYMR
EMGTVELLTREGEIDIAKRIEDGINQVQCSVAEYPEAITY
LLEQYDRVEAEEARLSDLITGFVDDPELAREKFAELRAQY
VVTRDTIKATAQEEILKLSEVFKQFRLVPKQFDYLVNSMR
VMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDT
WFNAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLT
IEQVKDINRRMSIGEAKARRAKKEMVEANLRLVISIAKKY
TNRGLQFLDLIQEGNIGLMKAVDKFEYRRGYKFSTYATWW
IRQAITRSIADQARTIRIPVHMIETINKLNRISRQMLQEM
GREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDD
EDSHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAR
EAKVLRMRFGIDMNTDYTLEEVGKQFDVTRERIRQIEAKA
LRKLRHPSRSEVLRSFLDD
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 573-592
type DNA_BIND
sequence LEEVGKQFDVTRERIRQIEA
description H-T-H motif => ECO:0000255|HAMAP-Rule:MF_00963
source Swiss-Prot : SWS_FT_FI1

24) 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

25) chain F
residue 562
type SITE
sequence R
description Interaction with anti-sigma factors
source Swiss-Prot : SWS_FT_FI2

26) chain L
residue 562
type SITE
sequence R
description Interaction with anti-sigma factors
source Swiss-Prot : SWS_FT_FI2

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

28) chain F
residue 403-416
type prosite
sequence DLIQEGNIGLMKAV
description SIGMA70_1 Sigma-70 factors family signature 1. DLIQeGnIGLMkAV
source prosite : PS00715

29) 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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