Structure of PDB 8sy6 Chain J

Receptor sequence
>8sy6J (length=1269) Species: 562 (Escherichia coli) [Search protein sequence]
EFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGPV
KDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHIW
FLKSLPSRIGLLLDMPLRDIERVLYFEGAEAIQALLKSMDLEQECEQLRE
ELKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFAT
SDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRR
GRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLR
LHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDIL
DEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFD
GDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYY
MTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGE
LVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRIL
GLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVA
EIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQ
EEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITAN
FREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTED
DCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNT
LLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKG
EAIGVIAAQSIGEPGTQLTMRTFHIGGAASRAAAESSIQVKNKGSIKLSN
VKSVVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVA
GGETVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVL
DSAERTAGGKDLRPALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDG
VQISSGDTLARIPQESGGTKDITGGLPRVADLFEARRPKEPAILAEISGV
ERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGVKINDKHIE
VIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANGKVGATYSR
DLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRGLKENVIVG
RLIPAGTGYAYHQDRMRRR
3D structure
PDB8sy6 A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase.
ChainJ
Resolution3.28 Å
3D
structure
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Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
Interaction with ligand
Site
#		 Ligand Ligand
chain		 Binding residues on receptor
(original residue number in PDB)		 Binding residues on receptor
(residue number reindexed from 1)		 Binding affinity
BS01 dna J R311 K334 R346 T790 A791 Y795 M932 R249 K272 R284 T728 A729 Y733 M870
BS02 rna J D462 D464 D400 D402
BS03 DG J L255 R259 L193 R197
BS04 ZN J C814 C898 C752 C836
BS05 ZN J C72 C85 E86 K87 C57 C70 E71 K72
BS06 MG J D460 D462 D464 D398 D400 D402
BS07 UTP J R425 D460 D462 M932 H936 R363 D398 D400 M870 H874
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003677 DNA binding
GO:0003899 DNA-directed 5'-3' RNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0016779 nucleotidyltransferase activity
GO:0034062 5'-3' RNA polymerase activity
GO:0046872 metal ion binding
Biological Process
GO:0006351 DNA-templated transcription
GO:0006352 DNA-templated transcription initiation
GO:0006879 intracellular iron ion homeostasis
GO:0009408 response to heat
GO:0031564 transcription antitermination
GO:0032784 regulation of DNA-templated transcription elongation
GO:0036460 cellular response to cell envelope stress
GO:0042128 nitrate assimilation
GO:0044780 bacterial-type flagellum assembly
GO:0046677 response to antibiotic
GO:0048870 cell motility
GO:0071973 bacterial-type flagellum-dependent cell motility
GO:0090605 submerged biofilm formation
GO:2000142 regulation of DNA-templated transcription initiation
Cellular Component
GO:0000345 cytosolic DNA-directed RNA polymerase complex
GO:0000428 DNA-directed RNA polymerase complex
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0008023 transcription elongation factor complex
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8sy6, PDBe:8sy6, PDBj:8sy6
PDBsum8sy6
PubMed38086811
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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