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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	skp
Gene Synonym(s)	hlpA, ECK0177, b0178, JW0173, firA, ompH^[1]^[2], ompH
Product Desc.	periplasmic chaperone^[3]^[2] Periplasmic molecular chaperone for outer membrane proteins; trimeric^[4]
Product Synonyms(s)	periplasmic chaperone^[1], B0178^[3]^[1], Skp^[3]^[1], OmpH^[3]^[1], HlpA^[3]^[1], HLP-I^[3]^[1] , ECK0177, hlpA, JW0173, ompH, b0178
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE^[3], ecfK-skp-lpxD-fabZ-lpxAB-rnhB-dnaE, hlpA-lpxD-fabZ-lpxA^[3]
Regulation/Activity
Quick Links
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Notes

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The reported binding to DNA was an artifact due to the cationic nature of Skp.^[4]

Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	skp
Mnemonic	seventeen kilodalton protein ^[5] 17-kilodalton protein
Synonyms	hlpA, ECK0177, b0178, JW0173, firA, ompH^[1]^[2], ompH
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	4.32 minutes	MG1655: 200482..200967 <gbrowseImage> name=NC_000913:200482..200967 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 200481..200966 <gbrowseImage> name=NC_012759:200481..200966 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 200482..200967 <gbrowseImage> name=NC_007779:200482..200967 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 174586..175071 <gbrowseImage> name=NC_010473:174586..175071 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	200542	Edman degradation	PMID:2167239 PMID:2843433 PMID:9298646
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource

Resource Type

Source

Notes/Reference

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (EcoliWiki Page)	GeneID:944861	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	HlpA
Synonyms	periplasmic chaperone^[1], B0178^[3]^[1], Skp^[3]^[1], OmpH^[3]^[1], HlpA^[3]^[1], HLP-I^[3]^[1] , ECK0177, hlpA, JW0173, ompH, b0178
Product description	periplasmic chaperone^[3]^[2] Periplasmic molecular chaperone for outer membrane proteins; trimeric^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	Aspect	Notes	Status
	GO:0042597	periplasmic space	PMID:1838129		C		Missing: evidence
	GO:0005515	protein binding	PMID:17928002	IDA: Inferred from Direct Assay	F	Skp is homotrimeric.	complete
	GO:0006457	protein folding	PMID:10455120	IMP: Inferred from Mutant Phenotype	P		complete
	GO:0030288	outer membrane-bounded periplasmic space	PMID:10455120	IDA: Inferred from Direct Assay	C		complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	glyS		PMID:15690043	Experiment(s):EBI-881988
Protein	hisS		PMID:15690043	Experiment(s):EBI-881988
Protein	rplE		PMID:15690043	Experiment(s):EBI-881988
Protein	rplI		PMID:15690043	Experiment(s):EBI-881988
Protein	rplM		PMID:15690043	Experiment(s):EBI-881988
Protein	rplO		PMID:15690043	Experiment(s):EBI-881988
Protein	rplS		PMID:15690043	Experiment(s):EBI-881988
Protein	rplU		PMID:15690043	Experiment(s):EBI-881988
Protein	rplV		PMID:15690043	Experiment(s):EBI-881988
Protein	rplX		PMID:15690043	Experiment(s):EBI-881988
Protein	rpsM		PMID:15690043	Experiment(s):EBI-881988
Protein	spoT		PMID:15690043	Experiment(s):EBI-881988
Protein	rnr		PMID:15690043	Experiment(s):EBI-881988
Protein	rplU		PMID:19402753	MALDI(Z-score):17.053160
Protein	rplX		PMID:19402753	MALDI(Z-score):17.053160
Protein	hisS		PMID:19402753	MALDI(Z-score):17.053160
Protein	Skp	Skp forms homotrimers
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Notes

Because Skp is a periplasmic chaperone, interaction data should be interpreted with caution. Many of the interactions reported large-scale interactome experiments using whole cell extracts ^[6] are with cytosolic proteins. Jachow et al ^[7] identified possible Skp substrates by examining interactions from periplasmic extracts.

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Evidence	Reference/Source
periplasm		From EcoCyc^[2]
Periplasm	PMID:2167239	EchoLocation:skp
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MKKWLLAAGL GLALATSAQA ADKIAIVNMG SLFQQVAQKT GVSNTLENEF KGRASELQRM ETDLQAKMKK LQSMKAGSDR TKLEKDVMAQ RQTFAQKAQA FEQDRARRSN EERGKLVTRI QTAVKSVANS QDIDLVVDAN AVAYNSSDVK DITADVLKQV K
Length	161
Mol. Wt	17.687 kDa
pI	10.1 (calculated)
Extinction coefficient	6,990 (calc based on 1 Y, 1 W, and 0 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
motif	1-20	UniProt Manual:Signal Peptides	UniProt:P0AEU7
Domain	6..161	PF03938 Outer membrane protein (OmpH-like)		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=skp taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16128171	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944861	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AEU7	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944861	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	Ecoli K-12	20.347+/-0.097	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.755670103	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	20120	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	10662	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	15549	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
yaeT-hlpA-lpxD-fabZ-lpxAB-rnhB-dnaE
hlpA-lpxD-fabZ-lpxA
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File:.jpg

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Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:200462..200502 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

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Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0178 (EcoliWiki Page)	NCBI GEO profiles for skp
microarray	GenExpDB:b0178 (EcoliWiki Page)	Summary of data for skp from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (200278..200555) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:C2^[8]
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Notes

Accessions Related to skp Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0178
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000001967 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000036446 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	HLPA	From SHIGELLACYC
E. coli O157	HLPA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF03938 Outer membrane protein (OmpH-like)
Superfamily (EcoliWiki Page)	SUPERFAMILY:111384
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.00 ^3.01 ^3.02 ^3.03 ^3.04 ^3.05 ^3.06 ^3.07 ^3.08 ^3.09 ^3.10 ^3.11 ^3.12 ^3.13 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Holck, A & Kleppe, K (1988) Cloning and sequencing of the gene for the DNA-binding 17K protein of Escherichia coli. Gene 67 117-24 PubMed
↑ Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ Jarchow, S et al. (2008) Identification of potential substrate proteins for the periplasmic Escherichia coli chaperone Skp. Proteomics 8 4987-94 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

skp:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to skp Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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