Reviewed, UniProtKB/Swiss-Prot P00579 (RPOD_ECOLI)

Names and origin

Protein names

Recommended name:
    RNA polymerase sigma factor rpoD
Alternative name(s):
    Sigma-70

Gene names

Name:	rpoD
Synonyms:	alt
Ordered Locus Names:	b3067, JW3039

Organism

Escherichia coli (strain K12) [Complete proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	613 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is not processed.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This is the primary sigma factor of this bacterium.
Sequence similarities	Belongs to the sigma-70 factor family.

Ontologies

Keywords
Biological process	Transcription Transcription regulation
Ligand	DNA-binding
Molecular function	Sigma factor
Technical term	3D-structure Complete proteome
Gene Ontology (GO)
Biological process	regulation of transcription, DNA-dependent Inferred from electronic annotation. Source: UniProtKB-KW transcription initiation Inferred from electronic annotation. Source: InterPro
Molecular function	protein binding Inferred from physical interaction. Source: IntAct sigma factor activity Inferred from electronic annotation. Source: UniProtKB-KW transcription factor activity Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
rpoC	P0A8T7	1	EBI-545104,EBI-543604

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 613

613

RNA polymerase sigma factor rpoD

PRO_0000093885

Regions

DNA binding

573 – 592

20

H-T-H motif By similarity

Motif

403 – 416

14

Polymerase core binding Potential

Experimental info

Sequence conflict

149

1

D → N in AAA24601. Ref.1

Secondary structure

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613

Helix Strand Turn

Details...

Helix

116 – 134

19

Helix

138 – 148

11

Turn

149 – 154

6

Helix

158 – 160

3

Beta strand

162 – 165

4

Turn

179 – 182

4

Turn

187 – 190

4

Helix

214 – 234

21

Helix

243 – 256

14

Beta strand

259 – 261

3

Helix

263 – 292

30

Helix

299 – 306

8

Turn

307 – 309

3

Helix

313 – 315

3

Helix

317 – 320

4

Helix

325 – 329

5

Helix

330 – 332

3

Helix

334 – 351

18

Helix

355 – 382

28

Helix

384 – 391

8

Beta strand

397 – 399

3

Helix

401 – 418

18

Helix

421 – 423

3

Helix

427 – 445

19

Sequences

	Sequence		Length	Mass (Da)
	P00579-1 [UniParc]. Last modified October 1, 1996. Version 2. Checksum: CA4F0E30DEC1703D	FASTA	613	70,263
	10 20 30 40 50 60 MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND MGIQVMEEAP 70 80 90 100 110 120 DADDLMLAEN TADEDAAEAA AQVLSSVESE IGRTTDPVRM YMREMGTVEL LTREGEIDIA 130 140 150 160 170 180 KRIEDGINQV QCSVAEYPEA ITYLLEQYDR VEAEEARLSD LITGFVDPNA EEDLAPTATH 190 200 210 220 230 240 VGSELSQEDL DDDEDEDEED GDDDSADDDN SIDPELAREK FAELRAQYVV TRDTIKAKGR 250 260 270 280 290 300 SHATAQEEIL KLSEVFKQFR LVPKQFDYLV NSMRVMMDRV RTQERLIMKL CVEQCKMPKK 310 320 330 340 350 360 NFITLFTGNE TSDTWFNAAI AMNKPWSEKL HDVSEEVHRA LQKLQQIEEE TGLTIEQVKD 370 380 390 400 410 420 INRRMSIGEA KARRAKKEMV EANLRLVISI AKKYTNRGLQ FLDLIQEGNI GLMKAVDKFE 430 440 450 460 470 480 YRRGYKFSTY ATWWIRQAIT RSIADQARTI RIPVHMIETI NKLNRISRQM LQEMGREPTP 490 500 510 520 530 540 EELAERMLMP EDKIRKVLKI AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL 550 560 570 580 590 600 RAATHDVLAG LTAREAKVLR MRFGIDMNTD YTLEEVGKQF DVTRERIRQI EAKALRKLRH 610 PSRSEVLRSF LDD

References

	« Hide 'large scale' referencesShow 'large scale' references »
[1]	"The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12." Burton Z.F., Burgess R.R., Lin J., Moore D., Holder S., Gross C.A. Nucleic Acids Res. 9:2889-2903(1981) [PubMed: 6269063] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA]. Strain: K12.
[2]	"The complete genome sequence of Escherichia coli K-12." Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y. Science 277:1453-1474(1997) [PubMed: 9278503] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / MG1655 / ATCC 47076.
[3]	"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110." Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T. Mol. Syst. Biol. 2:E1-E5(2006) [PubMed: 16738553] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase." Malhotra A., Severinova E., Darst S.A. Cell 87:127-136(1996) [PubMed: 8858155] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.6 ANGSTROMS) OF 113-446.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

J01687 Genomic DNA. Translation: AAA24601.1.
U28379 Genomic DNA. Translation: AAA89147.1.
U00096 Genomic DNA. Translation: AAC76103.1.
AP009048 Genomic DNA. Translation: BAE77118.1.

PIR

RNECS. A65095.

RefSeq

AP_003617.1.
NP_417539.1.

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1SIG	X-ray	2.60	A	114-448	[»]
1TLH	NMR	-	B	533-613	[»]
2P7V	X-ray	2.60	B	546-613	[»]

ModBase

Search...

Protein-protein interaction databases

DIP

DIP:10773N.

IntAct

P00579. 43 interactions.

STRING

P00579.

2-D gel databases

ECO2DBASE

B082.0. 6TH EDITION.

Proteomic databases

PRIDE

P00579.

Genome annotation databases

GeneID

947567.

GenomeReviews

Gene locus JW3039 in contig AP009048_GR.
Gene locus b3067 in contig U00096_GR.

KEGG

ecj:JW3039.
eco:b3067.

Organism-specific databases

EchoBASE

EB0889.

EcoGene

EG10896. rpoD.

CMR

Search...

Phylogenomic databases

HOGENOM

P00579.

OMA

HPSRSET

Enzyme and pathway databases

BioCyc

EcoCyc:RPOD-MON.
ECOL168927:B3067-MON.

Gene expression databases

Genevestigator

P00579.

Family and domain databases

InterPro

IPR014284. RNA_pol_sigma-70.
IPR000943. RNA_pol_sigma70.
IPR009042. RNA_pol_sigma70_r1_2.
IPR007627. RNA_pol_sigma70_r2.
IPR007624. RNA_pol_sigma70_r3.
IPR007630. RNA_pol_sigma70_r4.
IPR007631. RNA_pol_sigma_70_non-ess.
IPR007127. RNA_pol_sigma_70_r1.1.
IPR013325. RNA_pol_sigma_r2.
IPR013324. RNA_pol_sigma_r3_r4.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR011991. Wing_hlx_DNA_bd.
[Graphical view]

Gene3D

G3DSA:1.10.10.10. Wing_hlx_DNA_bd. 2 hits.

Pfam

PF04546. Sigma70_ner. 1 hit.
PF03979. Sigma70_r1_1. 1 hit.
PF00140. Sigma70_r1_2. 1 hit.
PF04542. Sigma70_r2. 1 hit.
PF04539. Sigma70_r3. 1 hit.
PF04545. Sigma70_r4. 1 hit.
[Graphical view]

PRINTS

PR00046. SIGMA70FCT.

TIGRFAMs

TIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.

PROSITE

PS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

RPOD_ECOLI

Accession

Primary (citable) accession number: P00579
Secondary accession number(s): Q2M9D8

Entry history

Integrated into UniProtKB/Swiss-Prot:	July 21, 1986
Last sequence update:	October 1, 1996
Last modified:	November 24, 2009
This is version 108 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes)