Structure of PDB 4ylo Chain R

Receptor sequence

>4yloR (length=497) Species: 562 (Escherichia coli) [Search protein sequence]

AAAQVLSSVESEIGRTTDPVRMYMREMGTVELLTREGEIDIAKRIEDGIN
QVQCSVAEYPEAITYLLEQYDRVEAEEARLSDLITGFVDPNAENSIDPEL
AREKFAELRAQYVVTRDTIKAKGRSHATAQEEILKLSEVFKQFRLVPKQF
DYLVNSMRVMMDRVRTQERLIMKLCVEQCKMPKKNFITLFTGNETSDTWF
NAAIAMNKPWSEKLHDVSEEVHRALQKLQQIEEETGLTIEQVKDINRRMS
IGEAKARRAKKEMVEANLRLVISIAKKYTNRGLQFLDLIQEGNIGLMKAV
DKFEYRRGYKFSTYATWWIRQAITRSIADQARTIRIPVHMIETINKLNRI
SRQMLQEMGREPTPEELAERMLMPEDKIRKVLKIAKEPISMETPIGDDED
SHLGDFIEDTTLELPLDSATTESLRAATHDVLAGLTAREAKVLRMRFGID
MNTDYTLEEVGKQFDVTRERIRQIEAKALRKLRHPSRSEVLRSFLDD

3D structure

PDB

4ylo Crystal Structures of the E. coli Transcription Initiation Complexes with a Complete Bubble.

Chain

Resolution

6.0 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

Enzymatic activity

Enzyme Commision number

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	R	V98 M102 L110 T112 N383 R385 L386 I388 S389 K392 F401 K418 F419 K426 S428 T429 Y430 T432 W434 Q437 R441 R451 P453 V454 T583 R584 R586	V20 M24 L32 T34 N267 R269 L270 I272 S273 K276 F285 K302 F303 K310 S312 T313 Y314 T316 W318 Q321 R325 R335 P337 V338 T467 R468 R470
BS02	dna	R	Y394 W433 Q437 H455 E458 N461 N464 R465 R468 D513 R562 T572 L573 E585 R588	Y278 W317 Q321 H339 E342 N345 N348 R349 R352 D397 R446 T456 L457 E469 R472

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003700	DNA-binding transcription factor activity
GO:0005515	protein binding
GO:0016987	sigma factor activity

	Biological Process
GO:0006351	DNA-templated transcription
GO:0006352	DNA-templated transcription initiation
GO:0006355	regulation of DNA-templated transcription
GO:0009408	response to heat
GO:0010468	regulation of gene expression
GO:0045892	negative regulation of DNA-templated transcription
GO:2000142	regulation of DNA-templated transcription initiation

	Cellular Component
GO:0000345	cytosolic DNA-directed RNA polymerase complex
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:1903865	sigma factor antagonist complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:4ylo, PDBe:4ylo, PDBj:4ylo
PDBsum	4ylo
PubMed	25866247
UniProt	P00579\|RPOD_ECOLI RNA polymerase sigma factor RpoD (Gene Name=rpoD)

[Back to BioLiP]