Structure of PDB 8f1i Chain M Binding Site BS02

Receptor Information
>8f1i Chain M (length=405) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QLAMTPQLQQAIRLLQLSTLELQQELQQALESNPLLEQIDYQGETTQTLQ
DYLMWQVELTPFSDTDRAIATSIVDAVDETGYLTVPLEDILESIGDEEID
IDEVEAVLKRIQRFDPVGVAAKDLRDCLLIQLSQFDKTTPWLEEARLIIS
DHLDLLANHDFRTLMRVTRLKEDVLKEAVNLIQSLDPRPGQSIQTGEPEY
VIPDVLVRKHNGHWTVELNSDSIPRLQINQHYASMCNNARNDGDSQFIRS
NLQDAKWLIKSLESRNDTLLRVSRCIVEQQQAFFEQGEEYMKPMVLADIA
QAVEMHESTISRVTTQKYLHSPRGIFELKYFFSSHVNTEGGGEASSTAIR
ALVKKLIAAENPAKPLSDSKLTSLLSEQGIMVARRTVAKYRESLSIPPSN
QRKQL
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]
PDB8f1i A general mechanism for transcription bubble nucleation in bacteria.
Resolution3.0 Å
Binding residue
(original residue number in PDB)		A22 R233 W328 S335 H377 S379 T380 S405 A454 R456 T457 K460 Y461
Binding residue
(residue number reindexed from 1)		A11 R162 W257 S264 H306 S308 T309 S334 A383 R385 T386 K389 Y390
Enzymatic activity
Enzyme Commision number ?
Gene Ontology
Molecular Function
GO:0000976 transcription cis-regulatory region binding
GO:0001216 DNA-binding transcription activator activity
GO:0003677 DNA binding
GO:0016779 nucleotidyltransferase activity
GO:0016987 sigma factor activity
Biological Process
GO:0006352 DNA-templated transcription initiation
GO:0006355 regulation of DNA-templated transcription
GO:0006525 arginine metabolic process
GO:0042128 nitrate assimilation
GO:0045893 positive regulation of DNA-templated transcription
GO:0048870 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:0032993 protein-DNA complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8f1i, PDBe:8f1i, PDBj:8f1i
PDBsum8f1i
PubMed36972428
UniProtP24255|RP54_ECOLI RNA polymerase sigma-54 factor (Gene Name=rpoN)

[Back to BioLiP]