Structure of PDB 8u3b Chain D Binding Site BS01

Receptor Information
>8u3b Chain D (length=1344) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPERDGLFCARIFGP
VKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMGHIELASPTAHI
WFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTNLERQQILTEEQ
YLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLREELNETNSETKR
KKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLVPLDGGRFATSD
LNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAVDALLDNGRRGR
AITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRSVITVGPYLRLH
QCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVEREEAVVWDILDE
VIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLVCAAYNADFDGD
QMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPSQDVVLGLYYMT
RDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRITEYEKDANGELV
AKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISKMLNTCYRILGL
KPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEIISEAEAEVAEI
QEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQTETVINRDGQEE
KQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGSIIETPITANFR
EGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDVAQDLVVTEDDC
GTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGTADILVPRNTLL
HEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDLARGHIINKGEA
IGVIAAQSIGEPGTQLTMAAESSIQVKNKGSIKLSNVKSVVNSSGKLVIT
SRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGETVANWDPHTMP
VITEVSGFVRFTDMIDGQTITRQTDELTGLSSLVVLDSAERTAGGKDLRP
ALKIVDAQGNDVLIPGTDMPAQYFLPGKAIVQLEDGVQISSGDTLARIPQ
EITGGLPRVADLFEARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDG
SDPYEEMIPKWRQLNVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRY
IVNEVQDVYRLQGVKINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEY
SRVKIANRELEANGKVGATYSRDLLGITKASLATESFISAASFQETTRVL
TEAAVAGKRDELRGLKENVIVGRLIPAGTGYAYHQDRMRRRAAG
Ligand information
>8u3b Chain 1 (length=69) [Search DNA sequence] [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
agtaaccaataaatggtatttaaaatgcaaattatcaggcgtaccctctt
tgcgaattcgcggcagcgg
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8u3b Structural basis for transcription activation by the nitrate-responsive regulator NarL.
Resolution3.23 Å
Binding residue
(original residue number in PDB)		Y46 R133 K1170 K1311
Binding residue
(residue number reindexed from 1)		Y32 R119 K1138 K1279
Enzymatic activity
Enzyme Commision number 2.7.7.6: DNA-directed RNA polymerase.
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:8u3b, PDBe:8u3b, PDBj:8u3b
PDBsum8u3b
PubMed38197271
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

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