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Expression|

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Standard Name	pepQ
Gene Synonym(s)	ECK3839, b3847, JW3823^[1], JW3823
Product Desc.	proline dipeptidase^[2]^[3] Proline dipeptidase; prolidase; Xaa-Pro dipeptidase^[4]
Product Synonyms(s)	proline dipeptidase^[1], B3847^[2]^[1], PepQ^[2]^[1] , ECK3839, JW3823, b3847
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): pepQ^[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	pepQ
Mnemonic	Peptidase
Synonyms	ECK3839, b3847, JW3823^[1], JW3823
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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	86.84 minutes, 86.84 minutes	MG1655: 4029184..4030515 <gbrowseImage> name=NC_000913:4029184..4030515 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4009534..4010865 <gbrowseImage> name=NC_012967:4009534..4010865 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3918853..3920184 <gbrowseImage> name=NC_012759:3918853..3920184 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3605520..3604189 <gbrowseImage> name=NC_007779:3604189..3605520 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4128104..4129435 <gbrowseImage> name=NC_010473:4128104..4129435 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
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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
ΔpepQ (Keio:JW3823)	deletion	deletion			PMID:16738554	Shigen CGSC10765^[5]
ΔpepQ::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔpepQ787::kan					PMID:16738554	CGSC:102290
pepQ			Resistant to	Resistant to toxic, valine containing peptide	PMID:355237	strain: CM89	table 3
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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
JW3823	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGAATCACTGGCCTCGCTCTA Primer 2:CCgGCCAGTTTCAGATCCCGGGT
9B11	Kohara Phage	Genobase	PMID:3038334
16G1	Kohara Phage	Genobase	PMID:3038334
fad-751::Tn10	Linked marker	CAG18496 = CGSC7465^[5]	est. P1 cotransduction: 94% ^[6] Synonyms:fadAB101::Tn10
zih-35::Tn10	Linked marker	CAG18495 = CGSC7467^[5]	est. P1 cotransduction: 24% ^[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:EG10698	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10698	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000690	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948335	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0692	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012569	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	PepQ
Synonyms	proline dipeptidase^[1], B3847^[2]^[1], PepQ^[2]^[1] , ECK3839, JW3823, b3847
Product description	proline dipeptidase^[2]^[3] Proline dipeptidase; prolidase; Xaa-Pro dipeptidase^[4]
EC number (for enzymes)	3.4.13.9^[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:0006508	proteolysis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001131	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:0008235	metalloexopeptidase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01279	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008235	metalloexopeptidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001131	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:0009987	cellular process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000994	P	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:0016805	dipeptidase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01279	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016805	dipeptidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0224	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	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:0043171	peptide catabolic process	PMID:355237	IGI: Inferred from Genetic Interaction	EcoliWiki:pepA EcoliWiki:pepB EcoliWiki:pepD EcoliWiki:pepN	P		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	fdoG	PMID:16606699	Experiment(s):EBI-1146793
Protein	kdpD	PMID:16606699	Experiment(s):EBI-1146793
Protein	yfdP	PMID:19402753	LCMS(ID Probability):97.9
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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
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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 MESLASLYKN HIATLQERTR DALARFKLDA LLIHSGELFN VFLDDHPYPF KVNPQFKAWV PVTQVPNCWL LVDGVNKPKL WFYLPVDYWH NVEPLPTSFW TEDVEVIALP KADGIGSLLP AARGNIGYIG PVPERALQLG IEASNINPKG VIDYLHYYRS FKTEYELACM REAQKMAVNG HRAAEEAFRS GMSEFDINIA YLTATGHRDT DVPYSNIVAL NEHAAVLHYT KLDHQAPEEM RSFLLDAGAE YNGYAADLTR TWSAKSDNDY AQLVKDVNDE QLALIATMKA GVSYVDYHIQ FHQRIAKLLR KHQIITDMSE EAMVENDLTG PFMPHGIGHP LGLQVHDVAG FMQDDSGTHL AAPAKYPYLR CTRILQPGMV LTIEPGIYFI ESLLAPWREG QFSKHFNWQK IEALKPFGGI RIEDNVVIHE NNVENMTRDL KLA
Length	443
Mol. Wt	50.176 kDa
pI	5.9 (calculated)
Extinction coefficient	73,800 - 74,175 (calc based on 20 Y, 8 W, and 3 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	168..430	PF00557 Metallopeptidase family M24		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=pepQ 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:16131693	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948335	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012569	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P21165	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10698	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10698	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948335	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000690	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0692	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	E. coli K-12 MC4100	6.90E+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	Ecoli K-12	49.867+/-0.281	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.082644628	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	2511	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	1223	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	1937	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)
pepQ
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Figure courtesy of RegulonDB

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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_000913:4029164..4029204 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:b3847 (EcoliWiki Page)	NCBI GEO profiles for pepQ
microarray	GenExpDB:b3847 (EcoliWiki Page)	Summary of data for pepQ 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 (4028479..4028797) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ10; Well:G12^[7]
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Notes

Accessions Related to pepQ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10698	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0692	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3847
EcoGene	EcoGene:EG10698	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000690	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012569	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
Arabidopsis thaliana	AT4G29500 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PEPQ	From SHIGELLACYC
E. coli O157	PEPQ	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
Panther (EcoliWiki Page)	PTHR10804:SF17
Superfamily (EcoliWiki Page)	SUPERFAMILY:55920
Pfam (EcoliWiki Page)	PF00557 Metallopeptidase family M24
EcoCyc	EcoCyc:EG10698	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10698	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000690	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0692	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012569	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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 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 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

pepQ:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

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Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

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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 pepQ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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