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

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P00579 (RPOD_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 140. 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) [Reference proteome] [HAMAP]

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	DNA-dependent transcription, initiation Inferred from electronic annotation. Source: InterPro response to heat Inferred from expression pattern PubMed 8349564. Source: EcoliWiki
Molecular_function	DNA binding Inferred from electronic annotation. Source: UniProtKB-KW sequence-specific DNA binding transcription factor activity Inferred from electronic annotation. Source: InterPro sigma factor activity Inferred from direct assay PubMed 4882047. Source: EcoliWiki
Complete GO annotation...

Binary interactions

With	Entry	#Exp.	IntAct	Notes
asiA	P32267	5	EBI-545104,EBI-2124737	From a different organism.
rpoC	P0A8T7	8	EBI-545104,EBI-543604
rsd	P0AFX4	8	EBI-545104,EBI-1134364

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] [Europe PMC] [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] [Europe PMC] [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] [Europe PMC] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[4]	"Escherichia coli proteome analysis using the gene-protein database." VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C. Electrophoresis 18:1243-1251(1997) [PubMed] [Europe PMC] [Abstract] Cited for: IDENTIFICATION BY 2D-GEL.
[5]	"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] [Europe PMC] [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.
YP_491259.1. NC_007779.1.

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	[»]
4IGC	X-ray	3.70	X/Y	1-613	[»]

ProteinModelPortal

P00579.

SMR

P00579. Positions 114-613.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-10773N.

IntAct

P00579. 43 interactions.

MINT

MINT-1220595.

STRING

511145.b3067.

Proteomic databases

PaxDb

P00579.

PRIDE

P00579.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC76103; AAC76103; b3067.
BAE77118; BAE77118; BAE77118.

GeneID

12932074.
947567.

KEGG

ecj:Y75_p2993.
eco:b3067.

PATRIC

32121550. VBIEscCol129921_3162.

Organism-specific databases

EchoBASE

EB0889.

EcoGene

EG10896. rpoD.

Phylogenomic databases

eggNOG

COG0568.

HOGENOM

HOG000270272.

K03086.

OMA

IEMNTDH.

ProtClustDB

PRK05658.

Enzyme and pathway databases

BioCyc

EcoCyc:RPOD-MONOMER.
ECOL316407:JW3039-MONOMER.
MetaCyc:RPOD-MONOMER.

Gene expression databases

Genevestigator

P00579.

Family and domain databases

Gene3D

1.10.10.10. 2 hits.

InterPro

IPR014284. RNA_pol_sigma-70_dom.
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_DNA-bd_dom.
[Graphical view]

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...

Other

BindingDB

P00579.

ChEMBL

CHEMBL5329.

EvolutionaryTrace

P00579.

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:	May 1, 2013
This is version 140 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

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

Other

Entry information

Relevant documents