Structure of PDB 8y6u Chain F

Receptor sequence

>8y6uF (length=496) Species: 562 (Escherichia coli)

AAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGIN
QVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAENSIDPEL
AREKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQF
DYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWF
NAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMS
IGEAKARRAKKEMVEANLRLVISIAKKYTRGLQFLDLIQEGNIGLMKAVD
KFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRIS
RQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDEDS
HLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGIDM
NTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD

3D structure

• PDB: 8y6u NMR analysis of a loop-bulge structure of UUCGA pentaloop.
• Chain: F
• Resolution: 3.97 Å

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	F	V98 R99 M102 G106 L110 R385 L386 S389 K392 K418 F419 E420 R423 Y425 K426 S428 T429 Y430 W433 W434 Q437 R441 R451 P453 M456 T583 E585 R586	V20 R21 M24 G28 L32 R269 L270 S273 K276 K301 F302 E303 R306 Y308 K309 S311 T312 Y313 W316 W317 Q320 R324 R334 P336 M339 T466 E468 R469
BS02	dna	F	Y394 R397 G398 I443 E458 K462 R465 T509 I511 G512 T572 L573 E585 R588	Y278 R280 G281 I326 E341 K345 R348 T392 I394 G395 T455 L456 E468 R471

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0016987 sigma factor activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription
• GO:0006352 DNA-templated transcription initiation
• GO:0006355 regulation of DNA-templated transcription
• GO:0010468 regulation of gene expression
• GO:2000142 regulation of DNA-templated transcription initiation

Cellular Component

• GO:0005737 cytoplasm

External links

• PDB: RCSB:8y6u, PDBe:8y6u, PDBj:8y6u
• PDBsum: 8y6u
• PubMed: 38039839
• UniProt: Q0P6L9