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Protein

DNA-binding protein StpA

Gene

stpA

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

Functioni

A DNA-binding protein that acts in a fashion similar to H-NS protein upon overexpression, represses a number of genes including the cryptic blg operon, hns, papB and the proU locus (PubMed:8890170). A subset of H-NS/StpA-regulated genes also require Hha for repression; Hha and Cnu (YdgT) increases the number of genes DNA bound by H-NS/StpA and may also modulate the oligomerization of the H-NS/StpA-complex (PubMed:23543115). Repression can be inhibited by dominant-negative mutants of StpA or H-NS (PubMed:8755860).3 Publications
(Microbial infection) Originally isolated as a suppressor of a splicing defect of the thymidylate synthase (td) gene from bacteriophage T4 (PubMed:1480493). Acts as an RNA chaperone, accelerating splicing of viral pre-mRNA. Binds preferentially to unstructured over structured RNA; does not have a detectable high-affinity RNA-binding site in the pre-mRNA. There do not seem to be any specific RNA targets in transcribed E.coli DNA (PubMed:17267410).2 Publications

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi112 – 117By similarity6

GO - Molecular functioni

  • DNA binding Source: EcoliWiki
  • RNA binding Source: UniProtKB-KW

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Chaperone

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, RNA-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG11554-MONOMER.
ECOL316407:JW2644-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
DNA-binding protein StpA
Alternative name(s):
H-NS homolog StpA
Gene namesi
Name:stpA1 Publication
Synonyms:hnsB
Ordered Locus Names:b2669, JW2644
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG11554. stpA.

Subcellular locationi

GO - Cellular componenti

  • cytosol Source: EcoCyc
  • nucleoid Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

No visible phenotype in rich medium; double hns-stpA mutants grow slower and have reduced viable cell counts compared to single hns mutants in MC1029 and MC4100 backgrounds (PubMed:8890170). In 0.3M NaCl a double hns-stpA deletion up-regulates 583 and down-regulates 86 genes, 363 of which are thought to have been horizontally acquired; 131 are also up-regulated in a double cnu-hha deletion (PubMed:23543115).2 Publications

Mutagenesis

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Mutagenesisi26L → P: Partial loss of repressor function when overexpressed in the absence of hns. 1 Publication1
Mutagenesisi65 – 134Missing : Partial loss of repressor function when overexpressed in the absence of hns. 1 PublicationAdd BLAST70
Mutagenesisi97Y → C: Partial loss of repressor function when overexpressed in the absence of hns. 1 Publication1
Mutagenesisi116P → S: Partial loss of repressor function when overexpressed in the absence of hns. 1 Publication1
Mutagenesisi126G → V: Higher RNA chaperone activity than wild-type, decreased ability to bind structured RNA. 1 Publication1

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00001685131 – 134DNA-binding protein StpAAdd BLAST134

Proteomic databases

PaxDbiP0ACG1.
PRIDEiP0ACG1.

Expressioni

Inductioni

Expressed at low levels at 37 degrees Celsius, barely detectable at 26 degrees Celsius; expression is repressed by hns and partially activated by lrp (PubMed:8890170).1 Publication

Interactioni

Subunit structurei

When overexpressed forms homodimers, can interact with the N-terminus (residues 1-64) of H-NS (PubMed:8755860). May interact with Hha and/or Cnu.Curated1 Publication

Binary interactionsi

WithEntry#Exp.IntActNotes
hnsP0ACF83EBI-551928,EBI-544934

Protein-protein interaction databases

BioGridi4262261. 7 interactors.
DIPiDIP-35951N.
IntActiP0ACG1. 23 interactors.
MINTiMINT-1247857.
STRINGi511145.b2669.

Structurei

Secondary structure

1134
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi117 – 124Combined sources8
Helixi129 – 131Combined sources3

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LRXNMR-A90-134[»]
ProteinModelPortaliP0ACG1.
SMRiP0ACG1.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi42 – 45Poly-Glu4

Domaini

Both the N-terminus (residues 1-76) and the C-terminus (residues 90-134) have RNA chaperone activity for splicing of td, a bacteriophage T4 pre-mRNA (PubMed:17267410).1 Publication

Sequence similaritiesi

Belongs to the histone-like protein H-NS family.Curated

Phylogenomic databases

eggNOGiENOG4108X73. Bacteria.
COG2916. LUCA.
HOGENOMiHOG000218473.
KOiK11685.
OMAiVNTWLEL.

Family and domain databases

Gene3Di1.10.287.1050. 1 hit.
4.10.430.10. 1 hit.
InterProiIPR027444. H-NS_C_dom.
IPR001801. Histone_HNS.
IPR027454. Histone_HNS_oligo_dom.
[Graphical view]
PfamiPF00816. Histone_HNS. 1 hit.
[Graphical view]
PIRSFiPIRSF002096. HnS. 1 hit.
SMARTiSM00528. HNS. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0ACG1-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSVMLQSLNN IRTLRAMARE FSIDVLEEML EKFRVVTKER REEEEQQQRE
60 70 80 90 100
LAERQEKIST WLELMKADGI NPEELLGNSS AAAPRAGKKR QPRPAKYKFT
110 120 130
DVNGETKTWT GQGRTPKPIA QALAEGKSLD DFLI
Length:134
Mass (Da):15,348
Last modified:November 22, 2005 - v1
Checksum:i5870BD95F144CE6A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69210 Genomic DNA. Translation: CAA49146.1.
U07823 Genomic DNA. Translation: AAA64940.1.
U00096 Genomic DNA. Translation: AAC75716.1.
AP009048 Genomic DNA. Translation: BAA16535.1.
PIRiJH0774.
RefSeqiNP_417155.1. NC_000913.3.
WP_000115383.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC75716; AAC75716; b2669.
BAA16535; BAA16535; BAA16535.
GeneIDi947130.
KEGGiecj:JW2644.
eco:b2669.
PATRICi32120728. VBIEscCol129921_2761.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X69210 Genomic DNA. Translation: CAA49146.1.
U07823 Genomic DNA. Translation: AAA64940.1.
U00096 Genomic DNA. Translation: AAC75716.1.
AP009048 Genomic DNA. Translation: BAA16535.1.
PIRiJH0774.
RefSeqiNP_417155.1. NC_000913.3.
WP_000115383.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2LRXNMR-A90-134[»]
ProteinModelPortaliP0ACG1.
SMRiP0ACG1.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4262261. 7 interactors.
DIPiDIP-35951N.
IntActiP0ACG1. 23 interactors.
MINTiMINT-1247857.
STRINGi511145.b2669.

Proteomic databases

PaxDbiP0ACG1.
PRIDEiP0ACG1.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC75716; AAC75716; b2669.
BAA16535; BAA16535; BAA16535.
GeneIDi947130.
KEGGiecj:JW2644.
eco:b2669.
PATRICi32120728. VBIEscCol129921_2761.

Organism-specific databases

EchoBASEiEB1515.
EcoGeneiEG11554. stpA.

Phylogenomic databases

eggNOGiENOG4108X73. Bacteria.
COG2916. LUCA.
HOGENOMiHOG000218473.
KOiK11685.
OMAiVNTWLEL.

Enzyme and pathway databases

BioCyciEcoCyc:EG11554-MONOMER.
ECOL316407:JW2644-MONOMER.

Miscellaneous databases

PROiP0ACG1.

Family and domain databases

Gene3Di1.10.287.1050. 1 hit.
4.10.430.10. 1 hit.
InterProiIPR027444. H-NS_C_dom.
IPR001801. Histone_HNS.
IPR027454. Histone_HNS_oligo_dom.
[Graphical view]
PfamiPF00816. Histone_HNS. 1 hit.
[Graphical view]
PIRSFiPIRSF002096. HnS. 1 hit.
SMARTiSM00528. HNS. 1 hit.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiSTPA_ECOLI
AccessioniPrimary (citable) accession number: P0ACG1
Secondary accession number(s): P30017
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 22, 2005
Last sequence update: November 22, 2005
Last modified: November 2, 2016
This is version 89 of the entry and version 1 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.