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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	prlC
Gene Synonym(s)	ECK3483, b3498, JW3465, opdA^[1], opdA
Product Desc.	oligopeptidase A^[2]^[3] Oligopeptidase A, zinc metalloprotease; involved in the degradation of cleaved signal peptides; suppressor allele of LamB signal sequence mutations; heat shock regulon; proteinase In, multifunctional protease^[4]
Product Synonyms(s)	oligopeptidase A^[1], B3498^[2]^[1], OpdA^[2]^[1], PrlC^[2]^[1] , ECK3483, JW3465, opdA, b3498
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yhiQ^[2]
Regulation/Activity
Quick Links
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Notes

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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	prlC
Mnemonic	Protein localization
Synonyms	ECK3483, b3498, JW3465, opdA^[1], opdA
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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	78.48 minutes	MG1655: 3643205..3641163 <gbrowseImage> name=NC_000913:3641163..3643205 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3575872..3573830 <gbrowseImage> name=NC_012967:3573830..3575872 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3529657..3531699 <gbrowseImage> name=NC_012759:3529657..3531699 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3995233..3997275 <gbrowseImage> name=NC_007779:3995233..3997275 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3740950..3738908 <gbrowseImage> name=NC_010473:3738908..3740950 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	3641166	Edman degradation	PMID:9792922
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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)	Reference	Availability	Comments
ΔprlC (Keio:JW3465)	deletion	deletion	PMID:16738554	Shigen CGSC10567^[5]
prlC::Tn5KAN-I-SceI (FB21240)	Insertion at nt 1400 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21240	contains pKD46
prlC::Tn5KAN-I-SceI (FB21241)	Insertion at nt 1400 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21241	does not contain pKD46
ΔprlC754::kan			PMID:16738554	CGSC:102462
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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
JW3465	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACGAATCCGTTACTGACTCC Primer 2:CCGCCCTTAATGCCGTAATGCTC
12E4	Kohara Phage	Genobase	PMID:3038334
6A4	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[5]	est. P1 cotransduction: 10% ^[6] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[5]	est. P1 cotransduction: % ^[6]
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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
EcoCyc	EcoCyc:EG11441	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11441	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001405	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948016	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1411	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011421	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	PrlC
Synonyms	oligopeptidase A^[1], B3498^[2]^[1], OpdA^[2]^[1], PrlC^[2]^[1] , ECK3483, JW3465, opdA, b3498
Product description	oligopeptidase A^[2]^[3] Oligopeptidase A, zinc metalloprotease; involved in the degradation of cleaved signal peptides; suppressor allele of LamB signal sequence mutations; heat shock regulon; proteinase In, multifunctional protease^[4]
EC number (for enzymes)	3.4.24.70^[1]
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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	with/from	Aspect	Notes	Status
	GO:0004222	metalloendopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001567	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001567	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008233	peptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0645	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008237	metallopeptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0482	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006465	signal peptide processing	PMID:3053642	IDA: Inferred from Direct Assay		P		complete
	GO:0005737	cytoplasm	PMID:9792922	TAS: Traceable Author Statement		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	References	Evidence
Protein	yjhR	PMID:16606699	Experiment(s):EBI-1146030
Protein	bcsZ	PMID:16606699	Experiment(s):EBI-1146030
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Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
cytoplasm
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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 MTNPLLTPFE LPPFSKILPE HVVPAVTKAL NDCRENVERV VAQGAPYTWE NLCQPLAEVD DVLGRIFSPV SHLNSVKNSP ELREAYEQTL PLLSEYSTWV GQHEGLYKAY RDLRDGDHYA TLNTAQKKAV DNALRDFELS GIGLPKEKQQ RYGEIATRLS ELGNQYSNNV LDATMGWTKL VTDEAELAGM PESALAAAKA QAEAKELEGY LLTLDIPSYL PVMTYCDNQA LREEMYRAYS TRASDQGPNA GKWDNSKVME EILALRHELA QLLGFENYAF KSLATKMAEN PQQVLDFLTD LAKRARPQGE KELAQLRAFA KAEFGVDELQ PWDIAYYSEK QKQHLYSISD EQLRPYFPEN KAVNGLFEVV KRIYGITAKE RKDVDVWHPD VRFFELYDEN NELRGSFYLD LYARENKRGG AWMDDCVGQM RKADGSLQKP VAYLTCNFNR PVNGKPALFT HDEVITLFHE FGHGLHHMLT RIETAGVSGI SGVPWDAVEL PSQFMENWCW EPEALAFISG HYETGEPLPK ELLDKMLAAK NYQAALFILR QLEFGLFDFR LHAEFRPDQG AKILETLAEI KKLVAVVPSP SWGRFPHAFS HIFAGGYAAG YYSYLWADVL AADAFSRFEE EGIFNRETGQ SFLDNILSRG GSEEPMDLFK RFRGREPQLD AMLEHYGIKG
Length	680
Mol. Wt	77.168 kDa
pI	5.1 (calculated)
Extinction coefficient	110,700 - 111,450 (calc based on 30 Y, 12 W, and 6 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
Domain	222..678	PF01432 Peptidase family M3		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=prlC taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16131370	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948016	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011421	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P27298	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11441	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11441	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948016	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001405	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1411	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	Reference(s)
Protein	E. coli K-12 MC4100	5.39E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	3082	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	908	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	2334	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)
yhiQ
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Figure courtesy of RegulonDB

</protect>

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_000913:3643185..3643225 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b3498 (EcoliWiki Page)	NCBI GEO profiles for prlC
microarray	GenExpDB:b3498 (EcoliWiki Page)	Summary of data for prlC 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 (3642727..3643025) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ04; Well:G7^[7]
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Notes

Accessions Related to prlC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11441	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1411	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3498
EcoGene	EcoGene:EG11441	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001405	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011421	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	ENSANGP00000020780 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000027508 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G65620 (score: 1.000; bootstrap: 100%) AT5G10540 (score: 0.749)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000022482 (score: 1.000; bootstrap: 99%) ENSBTAP00000027246 (score: 0.470)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00023765 (score: 1.000; bootstrap: 65%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00013997 (score: 1.000; bootstrap: 71%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000028637 (score: 1.000; bootstrap: 99%) ENSCAFP00000011160 (score: 0.564)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000017105 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040718-47 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040718-62 (score: 1.000; bootstrap: 100%) ZDB-CDNA-041010-216 (score: 0.422) ZDB-GENE-041010-216 (score: 0.422)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0219735 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0039252 (score: 1.000; bootstrap: 86%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA11189-PA (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000023776 (score: 1.000; bootstrap: 56%)	From Inparanoid:20070104
Homo sapiens	ENSP00000304467 (score: 1.000; bootstrap: 99%) ENSP00000339283 (score: 0.540)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000021713 (score: 1.000; bootstrap: 96%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000006146 (score: 1.000; bootstrap: 99%) ENSMODP00000024527 (score: 0.531)	From Inparanoid:20070104
Mus musculus	MGI:1354165 (score: 1.000; bootstrap: 99%) MGI:1923055 (score: 0.539)	From Inparanoid:20070104
Oryza gramene	Q6K9T1 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000028990 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000015853 (score: 1.000; bootstrap: 99%) ENSRNOP00000027045 (score: 0.523)	From Inparanoid:20070104
Saccharomyces cerevisiae	YCL057W (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC1F30c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000139045 (score: 1.000; bootstrap: 99%) NEWSINFRUP00000165285 (score: 0.408)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00025195001 (score: 1.000; bootstrap: 99%) GSTENP00006269001 (score: 0.399)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000048194 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	PRLC	From SHIGELLACYC
E. coli O157	PRLC	From ECOO157CYC
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Notes

Families

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

Database	Accession	Notes
Panther (EcoliWiki Page)	PTHR11804:SF7
Superfamily (EcoliWiki Page)	SUPERFAMILY:55486
Pfam (EcoliWiki Page)	PF01432 Peptidase family M3
EcoCyc	EcoCyc:EG11441	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11441	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001405	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1411	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011421	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 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 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

prlC:On One Page

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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 prlC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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