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Protein

RNA polymerase sigma-54 factor

Gene

rpoN

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is responsible for the expression of enzymes involved in arginine catabolism. The open complex (sigma-54 and core RNA polymerase) serves as the receptor for the receipt of the melting signal from the remotely bound activator protein GlnG(NtrC).

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi366 – 38520H-T-H motifBy similarityAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Nucleotidyltransferase, Sigma factor, Transferase

Keywords - Biological processi

Arginine metabolism, Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:RPON-MONOMER.
ECOL316407:JW3169-MONOMER.
MetaCyc:RPON-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma-54 factor
Gene namesi
Name:rpoN
Synonyms:glnF, ntrA
Ordered Locus Names:b3202, JW3169
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10898. rpoN.

Subcellular locationi

Keywords - Cellular componenti

DNA-directed RNA polymerase

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 477477RNA polymerase sigma-54 factorPRO_0000205529Add
BLAST

Proteomic databases

PaxDbiP24255.
PRIDEiP24255.

Expressioni

Gene expression databases

CollecTFiEXPREG_00000990.

Interactioni

Protein-protein interaction databases

BioGridi4259282. 23 interactions.
DIPiDIP-10776N.
IntActiP24255. 14 interactions.
MINTiMINT-1224654.
STRINGi511145.b3202.

Structurei

Secondary structure

1
477
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi416 – 4194Combined sources
Turni420 – 4223Combined sources
Helixi423 – 4297Combined sources
Helixi441 – 4477Combined sources
Turni448 – 4503Combined sources
Helixi454 – 46512Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2MT3NMR-A414-477[»]
ProteinModelPortaliP24255.
SMRiP24255. Positions 423-465.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi454 – 4629RPON box

Compositional bias

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Compositional biasi3 – 3937Gln-richAdd
BLAST

Sequence similaritiesi

Belongs to the sigma-54 factor family.Curated

Phylogenomic databases

eggNOGiENOG4105DTW. Bacteria.
COG1508. LUCA.
HOGENOMiHOG000071905.
InParanoidiP24255.
KOiK03092.
OMAiTQKFMHT.
OrthoDBiEOG60CWN7.
PhylomeDBiP24255.

Family and domain databases

InterProiIPR000394. RNA_pol_sigma_54.
IPR007046. RNA_pol_sigma_54_core-bd.
IPR007634. RNA_pol_sigma_54_DNA-bd.
[Graphical view]
PfamiPF00309. Sigma54_AID. 1 hit.
PF04963. Sigma54_CBD. 1 hit.
PF04552. Sigma54_DBD. 1 hit.
[Graphical view]
PIRSFiPIRSF000774. RpoN. 1 hit.
PRINTSiPR00045. SIGMA54FCT.
TIGRFAMsiTIGR02395. rpoN_sigma. 1 hit.
PROSITEiPS00717. SIGMA54_1. 1 hit.
PS00718. SIGMA54_2. 1 hit.
PS50044. SIGMA54_3. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P24255-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKQGLQLRLS QQLAMTPQLQ QAIRLLQLST LELQQELQQA LESNPLLEQI
60 70 80 90 100
DTHEEIDTRE TQDSETLDTA DALEQKEMPE ELPLDASWDT IYTAGTPSGT
110 120 130 140 150
SGDYIDDELP VYQGETTQTL QDYLMWQVEL TPFSDTDRAI ATSIVDAVDE
160 170 180 190 200
TGYLTVPLED ILESIGDEEI DIDEVEAVLK RIQRFDPVGV AAKDLRDCLL
210 220 230 240 250
IQLSQFDKTT PWLEEARLII SDHLDLLANH DFRTLMRVTR LKEDVLKEAV
260 270 280 290 300
NLIQSLDPRP GQSIQTGEPE YVIPDVLVRK HNGHWTVELN SDSIPRLQIN
310 320 330 340 350
QHYASMCNNA RNDGDSQFIR SNLQDAKWLI KSLESRNDTL LRVSRCIVEQ
360 370 380 390 400
QQAFFEQGEE YMKPMVLADI AQAVEMHEST ISRVTTQKYL HSPRGIFELK
410 420 430 440 450
YFFSSHVNTE GGGEASSTAI RALVKKLIAA ENPAKPLSDS KLTSLLSEQG
460 470
IMVARRTVAK YRESLSIPPS NQRKQLV
Length:477
Mass (Da):53,990
Last modified:February 1, 1994 - v2
Checksum:i1FAA4273A02B34FD
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti99 – 1035GTSGD → APAVT (PubMed:2203540).Curated
Sequence conflicti99 – 1035GTSGD → APAVT (PubMed:8444818).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57612 Genomic DNA. Translation: AAA62790.1.
D12938 Genomic DNA. Translation: BAA02315.1.
Z27094 Genomic DNA. Translation: CAA81617.1.
U12684 Genomic DNA. Translation: AAB60163.1.
U18997 Genomic DNA. Translation: AAA58004.1.
U00096 Genomic DNA. Translation: AAC76234.1.
AP009048 Genomic DNA. Translation: BAE77246.1.
PIRiI57054. A35695.
RefSeqiNP_417669.1. NC_000913.3.
WP_000809057.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC76234; AAC76234; b3202.
BAE77246; BAE77246; BAE77246.
GeneIDi947714.
KEGGiecj:JW3169.
eco:b3202.
PATRICi32121824. VBIEscCol129921_3296.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M57612 Genomic DNA. Translation: AAA62790.1.
D12938 Genomic DNA. Translation: BAA02315.1.
Z27094 Genomic DNA. Translation: CAA81617.1.
U12684 Genomic DNA. Translation: AAB60163.1.
U18997 Genomic DNA. Translation: AAA58004.1.
U00096 Genomic DNA. Translation: AAC76234.1.
AP009048 Genomic DNA. Translation: BAE77246.1.
PIRiI57054. A35695.
RefSeqiNP_417669.1. NC_000913.3.
WP_000809057.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2MT3NMR-A414-477[»]
ProteinModelPortaliP24255.
SMRiP24255. Positions 423-465.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259282. 23 interactions.
DIPiDIP-10776N.
IntActiP24255. 14 interactions.
MINTiMINT-1224654.
STRINGi511145.b3202.

Proteomic databases

PaxDbiP24255.
PRIDEiP24255.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC76234; AAC76234; b3202.
BAE77246; BAE77246; BAE77246.
GeneIDi947714.
KEGGiecj:JW3169.
eco:b3202.
PATRICi32121824. VBIEscCol129921_3296.

Organism-specific databases

EchoBASEiEB0891.
EcoGeneiEG10898. rpoN.

Phylogenomic databases

eggNOGiENOG4105DTW. Bacteria.
COG1508. LUCA.
HOGENOMiHOG000071905.
InParanoidiP24255.
KOiK03092.
OMAiTQKFMHT.
OrthoDBiEOG60CWN7.
PhylomeDBiP24255.

Enzyme and pathway databases

BioCyciEcoCyc:RPON-MONOMER.
ECOL316407:JW3169-MONOMER.
MetaCyc:RPON-MONOMER.

Miscellaneous databases

PROiP24255.

Gene expression databases

CollecTFiEXPREG_00000990.

Family and domain databases

InterProiIPR000394. RNA_pol_sigma_54.
IPR007046. RNA_pol_sigma_54_core-bd.
IPR007634. RNA_pol_sigma_54_DNA-bd.
[Graphical view]
PfamiPF00309. Sigma54_AID. 1 hit.
PF04963. Sigma54_CBD. 1 hit.
PF04552. Sigma54_DBD. 1 hit.
[Graphical view]
PIRSFiPIRSF000774. RpoN. 1 hit.
PRINTSiPR00045. SIGMA54FCT.
TIGRFAMsiTIGR02395. rpoN_sigma. 1 hit.
PROSITEiPS00717. SIGMA54_1. 1 hit.
PS00718. SIGMA54_2. 1 hit.
PS50044. SIGMA54_3. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor sigma 54."
    Sasse-Dwight S., Gralla J.D.
    Cell 62:945-954(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Physical map location of the rpoN gene of Escherichia coli."
    Imaishi H., Gomada M., Inouye S., Nakazawa A.
    J. Bacteriol. 175:1550-1551(1993) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  3. "Molecular analysis of the operon which encodes the RNA polymerase sigma factor sigma 54 of Escherichia coli."
    Jones D.H.A., Franklin C.F.H., Thomas C.M.
    Microbiology 140:1035-1043(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12.
  4. "Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. Enzyme IIANtr affects growth on organic nitrogen and the conditional lethality of an erats mutant."
    Powell B.S., Court D.L., Inada T., Nakamura Y., Michotey V., Cui X., Reizer A., Saier M.H. Jr., Reizer J.
    J. Biol. Chem. 270:4822-4839(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  6. "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.

Entry informationi

Entry nameiRP54_ECOLI
AccessioniPrimary (citable) accession number: P24255
Secondary accession number(s): Q2M910
Entry historyi
Integrated into UniProtKB/Swiss-Prot: March 1, 1992
Last sequence update: February 1, 1994
Last modified: January 20, 2016
This is version 127 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.