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Product(s) |

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Standard Name	prpC
Gene Synonym(s)	ECK0330, b0333, JW0324, yahS, yzzD^[1], yzzD
Product Desc.	G6198^[2]^[3]; Component of methylcitrate synthase^[3] 2-Methylcitrate synthase; propionate catabolism via 2-methlycitrate cycle, characterized primarily in Salmonella^[4]
Product Synonyms(s)	2-methylcitrate synthase^[1], B0333^[2]^[1], YahS^[2]^[1], YzzD^[2]^[1], PrpC^[2]^[1] , ECK0330, JW0324, yahS, yzzD, b0333
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): prpB^[2], prpBCDE^[2]
Regulation/Activity
Quick Links
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Notes

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Repressed during biofilm formation. Crp regulon.^[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	prpC
Mnemonic	Propionate
Synonyms	ECK0330, b0333, JW0324, yahS, yzzD^[1], yzzD
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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	7.53 minutes	MG1655: 349236..350405 <gbrowseImage> name=NC_000913:349236..350405 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 322662..323831 <gbrowseImage> name=NC_012967:322662..323831 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 349236..350405 <gbrowseImage> name=NC_007779:349236..350405 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
prpC(del) (Keio:JW0324)	deletion	deletion			PMID:16738554	Shigen CGSC8521^[5]
prpC::Tn5KAN-I-SceI (FB20154)	Insertion at nt 1007 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20154	contains pKD46
prpC::Tn5KAN-I-SceI (FB20155)	Insertion at nt 1007 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20155	does not contain pKD46
prpC(del)::kan	deletion		Biolog:respiration	unable to respire a-Hydroxybutyrate	PMID:16095938
prpC(del)::kan	deletion		Biolog:respiration	unable to respire L-Asparagine	PMID:16095938
prpC(del)::kan	deletion		Biolog:respiration	unable to respire L-Aspartate	PMID:16095938
prpC774(del)::kan					PMID:16738554	CGSC:102484
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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
JW0324	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCGACACAACGATCCTGCA Primer 2:CCCTGGCGCTTATCCAGCGCGAC
9F1	Kohara Phage	Genobase	PMID:3038334
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[5]	est. P1 cotransduction: % ^[6]
lacI3042::Tn10	Linked marker	CAG18439 = CGSC7334^[5]	est. P1 cotransduction: 54% ^[6] Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).
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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:G6198	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11756	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002815	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947528	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1706	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001148	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	PrpC
Synonyms	2-methylcitrate synthase^[1], B0333^[2]^[1], YahS^[2]^[1], YzzD^[2]^[1], PrpC^[2]^[1] , ECK0330, JW0324, yahS, yzzD, b0333
Product description	G6198^[2]^[3]; Component of methylcitrate synthase^[3] 2-Methylcitrate synthase; propionate catabolism via 2-methlycitrate cycle, characterized primarily in Salmonella^[4]
EC number (for enzymes)	2.3.3.1^[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:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011278	C	Seeded from EcoCyc (v14.0)	complete
	GO:0019679	propionate metabolic process, methylcitrate cycle	PMID:9325432	IDA: Inferred from Direct Assay		P		complete
	GO:0006099	tricarboxylic acid cycle	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019810	P	Seeded from EcoCyc (v14.0)	complete
	GO:0044262	cellular carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002020	P	Seeded from EcoCyc (v14.0)	complete
	GO:0050440	2-methylcitrate synthase activity	PMID:9325432	IDA: Inferred from Direct Assay		F		complete
	GO:0044262	cellular carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011278	P	Seeded from EcoCyc (v14.0)	complete
	GO:0044262	cellular carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016141	P	Seeded from EcoCyc (v14.0)	complete
	GO:0044262	cellular carbohydrate metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016142	P	Seeded from EcoCyc (v14.0)	complete
	GO:0050440	2-methylcitrate synthase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:2.3.3.5	F	Seeded from EcoCyc (v14.0)	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	Subunits of methylcitrate synthase	could be indirect
Protein	napC		PMID:16606699	Experiment(s):EBI-1136274
Protein	nadE		PMID:16606699	Experiment(s):EBI-1136274
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Notes

Localization

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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 MSDTTILQNS THVIKPKKSV ALSGVPAGNT ALCTVGKSGN DLHYRGYDIL DLAKHCEFEE VAHLLIHGKL PTRDELAAYK TKLKALRGLP ANVRTVLEAL PAASHPMDVM RTGVSALGCT LPEKEGHTVS GARDIADKLL ASLSSILLYW YHYSHNGERI QPETDDDSIG GHFLHLLHGE KPSQSWEKAM HISLVLYAEH EFNASTFTSR VIAGTGSDMY SAIIGAIGAL RGPKHGGANE VSLEIQQRYE TPDEAEADIR KRVENKEVVI GFGHPVYTIA DPRHQVIKRV AKQLSQEGGS LKMYNIADRL ETVMWESKKM FPNLDWFSAV SYNMMGVPTE MFTPLFVIAR VTGWAAHIIE QRQDNKIIRP SANYVGPEDR PFVALDKRQ
Length	389
Mol. Wt	43.102 kDa
pI	7.1 (calculated)
Extinction coefficient	46,870 - 47,245 (calc based on 13 Y, 5 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	22..370	PF00285 Citrate synthase		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=prpC 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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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:16128318	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947528	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001148	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P31660	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6198	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11756	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947528	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002815	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1706	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 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	1^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
prpB
prpBCDE
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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_000913:349216..349256 source=MG1655 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:b0333 (EcoliWiki Page)	NCBI GEO profiles for prpC
microarray	GenExpDB:b0333 (EcoliWiki Page)	Summary of data for prpC 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 (348913..349241) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ13; Well:D3^[7]
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Notes

Accessions Related to prpC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6198	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1706	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0333
EcoGene	EcoGene:EG11756	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002815	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001148	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	ENSANGP00000015768 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000034681 (score: 1.000; bootstrap: 100%) ENSAPMP00000009152 (score: 0.174)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000005730 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00031330 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00000833 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000000167 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000000330 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030131-1058 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-1132 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0220637 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0026708 (score: 1.000; bootstrap: 100%) FBgn0037988 (score: 0.394)	From Inparanoid:20070104
Drosophila pseudoobscura	GA17736-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000342056 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000003339 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:88529 (score: 1.000; bootstrap: 100%) MGI:1919082 (score: 0.922)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000008664 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000034921 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YCR005C (score: 1.000; bootstrap: 100%) YNR001C (score: 0.792) YPR001W (score: 0.341)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC6C34 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000127671 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00023547001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000009670 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	PRPC	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)	PF00285 Citrate synthase
Superfamily (EcoliWiki Page)	SUPERFAMILY:48256
EcoCyc	EcoCyc:G6198	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11756	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002815	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1706	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001148	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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 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.
↑ ^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

prpC: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 prpC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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