Structure of PDB 8ree Chain D Binding Site BS02

Receptor Information
>8ree Chain D (length=1330) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LLKFLKAQTKTEEFDAIKIALASPDMIRSWSFGEVKKPETINYRTFKPER
DGLFCARIFGPVKDYECLCGKYKRLKHRGVICEKCGVEVTQTKVRRERMG
HIELASPTAHIWFLKSLPSRIGLLLDMPLRDIERVLYFESYVVIEGGMTN
LERQQILTEEQYLDALEEFGDEFDAKMGAEAIQALLKSMDLEQECEQLRE
ELNETNSETKRKKLTKRIKLLEAFVQSGNKPEWMILTVLPVLPPDLRPLV
PLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAAPDIIVRNEKRMLQEAV
DALLDNGRRGRAITGSNKRPLKSLADMIKGKQGRFRQNLLGKRVDYSGRS
VITVGPYLRLHQCGLPKKMALELFKPFIYGKLELRGLATTIKAAKKMVER
EEAVVWDILDEVIREHPVLLNRAPTLHRLGIQAFEPVLIEGKAIQLHPLV
CAAYNADFDGDQMAVHVPLTLEAQLEARALMMSTNNILSPANGEPIIVPS
QDVVLGLYYMTRDCVNAKGEGMVLTGPKEAERLYRSGLASLHARVKVRIT
EYEKDANGELVAKTSLKDTTVGRAILWMIVPKGLPYSIVNQALGKKAISK
MLNTCYRILGLKPTVIFADQIMYTGFAYAARSGASVGIDDMVIPEKKHEI
ISEAEAEVAEIQEQFQSGLVTAGERYNKVIDIWAAANDRVSKAMMDNLQT
ETVINRDGQEEKQVSFNSIYMMADSGARGSAAQIRQLAGMRGLMAKPDGS
IIETPITANFREGLNVLQYFISTHGARKGLADTALKTANSGYLTRRLVDV
AQDLVVTEDDCGTHEGIMMTPVIEGGDVKEPLRDRVLGRVTAEDVLKPGT
ADILVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDTDFGVCAHCYGRDL
ARGHIINKGEAIGVIAAQSIGEPGTQLTMAAESSIQVKNKGSIKLSNVKS
VVNSSGKLVITSRNTELKLIDEFGRTKESYKVPYGAVLAKGDGEQVAGGE
TVANWDPHTMPVITEVSGFVRFTDMIDGQTITRQSSLVVLDSAERRPALK
IVDAQGNDVAQYFLPGKAIVQLEDGVQISSGDTLARIPQGGLPRVADLFE
ARRPKEPAILAEISGIVSFGKETKGKRRLVITPVDGSDPYEEMIPKWRQL
NVFEGERVERGDVISDGPEAPHDILRLRGVHAVTRYIVNEVQDVYRLQGV
KINDKHIEVIVRQMLRKATIVNAGSSDFLEGEQVEYSRVKIANRELEANG
KVGATYSRDLLGITKASLATESFISAASFQETTRVLTEAAVAGKRDELRG
LKENVIVGRLIPAGTGYAYHQDRMRRRAAG
Ligand information
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8ree Structural basis of sigma 54 displacement and promoter escape in bacterial transcription.
Resolution3.8 Å
Binding residue
(original residue number in PDB)		P251 R322 R425 D462 D464
Binding residue
(residue number reindexed from 1)		P248 R319 R422 D459 D461
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8ree, PDBe:8ree, PDBj:8ree
PDBsum8ree
PubMed38170755
UniProtP0A8T7|RPOC_ECOLI DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)

[Back to BioLiP]