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Standard Name	prpB
Gene Synonym(s)	ECK0329, b0331, JW0323, yahQ^[1], yahQ
Product Desc.	G6196^[2]^[3]; Component of 2-methylisocitrate lyase^[3] 2-Methylisocitrate lyase; propionate catabolism via 2-methlycitrate cycle, characterized primarily in Salmonella^[4]
Product Synonyms(s)	2-methylisocitrate lyase^[1], B0331^[2]^[1], YahQ^[2]^[1], PrpB^[2]^[1] , ECK0329, JW0323, yahQ, b0331
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	prpB
Mnemonic	Propionate
Synonyms	ECK0329, b0331, JW0323, yahQ^[1], yahQ
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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	7.5 minutes	MG1655: 347906..348796 <gbrowseImage> name=NC_000913:347906..348796 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 321332..322222 <gbrowseImage> name=NC_012967:321332..322222 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 347906..348796 <gbrowseImage> name=NC_007779:347906..348796 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

prpB(del) (Keio:JW0323)

deletion

PMID:16738554

Shigen

CGSC8520^[5]

prpB773(del)::kan

PMID:16738554

CGSC:102482

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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
JW0323	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCTCTACACTCTCCAGGTAA Primer 2:CCTTTCACCTGGCTACGGGCAAA
1F6	Kohara Phage	Genobase	PMID:3038334
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: 51% ^[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:G6196	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13601	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002814	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944990	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3370	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001138	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	PrpB
Synonyms	2-methylisocitrate lyase^[1], B0331^[2]^[1], YahQ^[2]^[1], PrpB^[2]^[1] , ECK0329, JW0323, yahQ, b0331
Product description	G6196^[2]^[3]; Component of 2-methylisocitrate lyase^[3] 2-Methylisocitrate lyase; propionate catabolism via 2-methlycitrate cycle, characterized primarily in Salmonella^[4]
EC number (for enzymes)	4.1.3.30^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000918	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015813	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018523	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000918	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018523	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016829	lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0456	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046421	methylisocitrate lyase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.3.30	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 2-methylisocitrate lyase	could be indirect
Protein	cydC		PMID:16606699	Experiment(s):EBI-1136261
Protein	mukB		PMID:16606699	Experiment(s):EBI-1136261
Protein	yhaJ		PMID:16606699	Experiment(s):EBI-1136261
Protein	yjdA		PMID:16606699	Experiment(s):EBI-1136261
Protein	lacZ		PMID:16606699	Experiment(s):EBI-1136261
Protein	carA		PMID:16606699	Experiment(s):EBI-1136261
Protein	nadE		PMID:16606699	Experiment(s):EBI-1136261
Protein	pepD		PMID:16606699	Experiment(s):EBI-1136261
Protein	metH		PMID:16606699	Experiment(s):EBI-1136261
Protein	groL		PMID:16606699	Experiment(s):EBI-1136261
Protein	narZ		PMID:16606699	Experiment(s):EBI-1136261
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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 MSLHSPGKAF RAALTKENPL QIVGTINANH ALLAQRAGYQ AIYLSGGGVA AGSLGLPDLG ISTLDDVLTD IRRITDVCSL PLLVDADIGF GSSAFNVART VKSMIKAGAA GLHIEDQVGA KRCGHRPNKA IVSKEEMVDR IRAAVDAKTD PDFVIMARTD ALAVEGLDAA IERAQAYVEA GAEMLFPEAI TELAMYRQFA DAVQVPILAN ITEFGATPLF TTDELRSAHV AMALYPLSAF RAMNRAAEHV YNVLRQEGTQ KSVIDTMQTR NELYESINYY QYEEKLDNLF ARSQVK
Length	296
Mol. Wt	32.134 kDa
pI	5.5 (calculated)
Extinction coefficient	14,900 - 15,150 (calc based on 10 Y, 0 W, and 2 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
Initiator Methionine	1	Removed	UniProt:P77541
Domain	71..213	PF00463 Isocitrate lyase family		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=prpB 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:16128316	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944990	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001138	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77541	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6196	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13601	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944990	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002814	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3370	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	0^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_000913:347886..347926 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:b0331 (EcoliWiki Page)	NCBI GEO profiles for prpB
microarray	GenExpDB:b0331 (EcoliWiki Page)	Summary of data for prpB 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 (347590..347973) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:A5^[7]
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Notes

Accessions Related to prpB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6196	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3370	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0331
EcoGene	EcoGene:EG13601	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002814	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001138	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	ENSANGP00000026026 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G21440 (score: 1.000; bootstrap: 87%) AT1G77060 (score: 0.784)	From Inparanoid:20070104
Oryza gramene	Q7F8Y3 (score: 1.000; bootstrap: 100%) Q7X8I9 (score: 1.000; bootstrap: 100%) Q7XLP7 (score: 0.428)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000018511 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	PRPB	From ECOO157CYC
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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00463 Isocitrate lyase family
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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 ^2.9 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

prpB: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 prpB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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