RNA polymerase sigma factor rpoD - Escherichia coli (strain K12)

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P00579 (RPOD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 129. History...

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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)

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia

Protein attributes

Sequence length	613 AA.
Sequence status	Complete.
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 Reference proteome
Gene Ontology (GO)
Biological process	response to heat Inferred from expression pattern. Source: EcoliWiki transcription initiation, DNA-dependent Inferred from electronic annotation. Source: InterPro
Molecular function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW protein binding Inferred from physical interaction. Source: IntAct sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: InterPro sigma factor activity Inferred from direct assay. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
rpoC	P0A8T7	8	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

H-T-H motif By similarity

Motif

403 – 416

Polymerase core binding Potential

Experimental info

Sequence conflict

149

D → N in AAA24601. Ref.1

Secondary structure

613

Helix Strand Turn

Details...

Sequences

Sequence

Length

Mass (Da)

Tools

P00579 [UniParc].

Last modified October 1, 1996. Version 2.
Checksum: CA4F0E30DEC1703D
Show »

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

« Hide

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

EMBL
GenBank
DDBJ

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

NP_417539.1. NC_000913.2.

3D structure databases

PDBe
RCSB PDB
PDBj

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	[»]
3IYD	electron microscopy	-	F	1-613	[»]
3T72	X-ray	4.33	o/q	533-609	[»]

ProteinModelPortal

P00579.

SMR

P00579. Positions 4-64, 114-613.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10773N.

IntAct

P00579. 43 interactions.

MINT

MINT-1220595.

2D gel databases

ECO2DBASE

B082.0. 6TH EDITION.

Proteomic databases

PRIDE

P00579.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

EBESCT00000001124; EBESCP00000001124; EBESCG00000000933.
EBESCT00000001125; EBESCP00000001125; EBESCG00000000933.
EBESCT00000001126; EBESCP00000001126; EBESCG00000000933.
EBESCT00000001127; EBESCP00000001127; EBESCG00000000933.
EBESCT00000001128; EBESCP00000001128; EBESCG00000000933.
EBESCT00000001129; EBESCP00000001129; EBESCG00000000933.
EBESCT00000001130; EBESCP00000001130; EBESCG00000000933.
EBESCT00000017672; EBESCP00000016963; EBESCG00000016728.

GeneID

947567.

GenomeReviews

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

KEGG

ecj:JW3039.
eco:b3067.

PATRIC

32121550. VBIEscCol129921_3162.

Organism-specific databases

EchoBASE

EB0889.

EcoGene

EG10896. rpoD.

Phylogenomic databases

eggNOG

COG0568.

GeneTree

EBGT00050000009820.

HOGENOM

HBG745096.

OMA

HPSRSET.

PhylomeDB

P00579.

ProtClustDB

PRK05658.

Enzyme and pathway databases

BioCyc

EcoCyc:RPOD-MONOMER.
MetaCyc:RPOD-MONOMER.

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. WHTH_trsnscrt_rep_DNA-bd.
[Graphical view]

Gene3D

G3DSA:1.10.10.10. Wing_hlx_DNA_bd. 2 hits.

K03086.

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.

SUPFAM

SSF88946. Sigma_r2. 1 hit.
SSF88659. Sigma_r3_r4. 2 hits.

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:	January 25, 2012
This is version 129 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Names·Attributes·General annotation·Ontologies·Interactions·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Binary interactions

With

Entry

#Exp.

IntAct

Notes

Sequence annotation (Features)

Molecule processing

Regions

Experimental info

Secondary structure

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

2D gel databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents