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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	prpD
Gene Synonym(s)	ECK0331, b0334, JW0325, acnC, yahT^[1], yahT
Product Desc.	G6199^[2]^[3] 2-Methylcitrate dehydratase, 2-methylisocitrate hydratase; propionate catabolism via 2-methlycitrate cycle; active on citrate and isocitrate; responsible for residual apparent aconitase activity in acnAB double mutant; monomeric iron-sulfur protein^[4]
Product Synonyms(s)	2-methylcitrate dehydratase^[1], B0334^[2]^[1], AcnC^[2]^[1], YahT^[2]^[1], PrpD^[2]^[1] , acnC, ECK0331, JW0325, yahT, b0334
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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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	prpD
Mnemonic	Propionate
Synonyms	ECK0331, b0334, JW0325, acnC, yahT^[1], yahT
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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	7.55 minutes	MG1655: 350439..351890 <gbrowseImage> name=NC_000913:350439..351890 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 323865..325316 <gbrowseImage> name=NC_012967:323865..325316 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 350439..351890 <gbrowseImage> name=NC_007779:350439..351890 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
prpD(del) (Keio:JW0325)	deletion	deletion			PMID:16738554	Shigen CGSC8522^[5]
prpD::Tn5KAN-I-SceI (FB20156)	Insertion at nt 762 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20156	contains pKD46
prpD::Tn5KAN-I-SceI (FB20157)	Insertion at nt 762 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20157	does not contain pKD46
prpD(del)::kan	deletion		Biolog:respiration	unable to respire a-Hydroxybutyrate	PMID:16095938
prpD(del)::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
prpD775(del)::kan					PMID:16738554	CGSC:102486
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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
JW0325	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCAGCTCAAATCAACAACAT Primer 2:CCAATGACGTACAGGTCGAGATA
9F1	Kohara Phage	Genobase	PMID:3038334
10A6	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: 56% ^[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:G6199	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13603	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002816	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945931	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3371	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001152	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	PrpD
Synonyms	2-methylcitrate dehydratase^[1], B0334^[2]^[1], AcnC^[2]^[1], YahT^[2]^[1], PrpD^[2]^[1] , acnC, ECK0331, JW0325, yahT, b0334
Product description	G6199^[2]^[3] 2-Methylcitrate dehydratase, 2-methylisocitrate hydratase; propionate catabolism via 2-methlycitrate cycle; active on citrate and isocitrate; responsible for residual apparent aconitase activity in acnAB double mutant; monomeric iron-sulfur protein^[4]
EC number (for enzymes)	4.2.1.79^[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				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	F	Seeded from EcoCyc (v14.0)	complete
	GO:0047547	2-methylcitrate dehydratase activity	PMID:12473114	IDA: Inferred from Direct Assay		F		complete
	GO:0019543	propionate catabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005656	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019679	propionate metabolic process, methylcitrate cycle	PMID:12473114	IDA: Inferred from Direct Assay		P		complete
	GO:0019629	propionate catabolic process, 2-methylcitrate cycle	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012705	P	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:0047547	2-methylcitrate dehydratase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005656	F	Seeded from EcoCyc (v14.0)	complete
	GO:0047547	2-methylcitrate dehydratase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012705	F	Seeded from EcoCyc (v14.0)	complete
	GO:0047547	2-methylcitrate dehydratase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.79	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0411	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051537	2 iron, 2 sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012705	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051537	2 iron, 2 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0001	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	References	Evidence
Protein	nadE	PMID:16606699	Experiment(s):EBI-1136278
Protein	groL	PMID:16606699	Experiment(s):EBI-1136278
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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 MSAQINNIRP EFDREIVDIV DYVMNYEISS KVAYDTAHYC LLDTLGCGLE ALEYPACKKL LGPIVPGTVV PNGVRVPGTQ FQLDPVQAAF NIGAMIRWLD FNDTWLAAEW GHPSDNLGGI LATADWLSRN AVASGKAPLT MKQVLTAMIK AHEIQGCIAL ENSFNRVGLD HVLLVKVAST AVVAEMLGLT REEILNAVSL AWVDGQSLRT YRHAPNTGTR KSWAAGDATS RAVRLALMAK TGEMGYPSAL TAPVWGFYDV SFKGESFRFQ RPYGSYVMEN VLFKISFPAE FHSQTAVEAA MTLYEQMQAA GKTAADIEKV TIRTHEACIR IIDKKGPLNN PADRDHCIQY MVAIPLLFGR LTAADYEDNV AQDKRIDALR EKINCFEDPA FTADYHDPEK RAIANAITLE FTDGTRFEEV VVEYPIGHAR RRQDGIPKLV DKFKINLARQ FPTRQQQRIL EVSLDRARLE QMPVNEYLDL YVI
Length	483
Mol. Wt	53.952 kDa
pI	5.8 (calculated)
Extinction coefficient	63,830 - 64,705 (calc based on 17 Y, 7 W, and 7 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:P77243
Domain	13..475	PF03972 MmgE/PrpD 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=prpD taxon=562,83333 </beststructure>

Models

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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:16128319	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945931	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001152	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77243	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6199	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13603	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945931	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002816	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3371	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	1^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_000913:350419..350459 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:b0334 (EcoliWiki Page)	NCBI GEO profiles for prpD
microarray	GenExpDB:b0334 (EcoliWiki Page)	Summary of data for prpD 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
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Notes

Accessions Related to prpD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6199	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3371	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0334
EcoGene	EcoGene:EG13603	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002816	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001152	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
Canis familiaris	ENSCAFP00000007552 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0191366 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000027300 (score: 1.000; bootstrap: 100%) ENSGALP00000012177 (score: 0.504)	From Inparanoid:20070104
Homo sapiens	ENSP00000218979 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000001357 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:103206 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000013182 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YPR002W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000143097 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000129866 (score: 0.485) NEWSINFRUP00000178984 (score: 0.147)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00027937001 (score: 1.000; bootstrap: 100%) GSTENP00017050001 (score: 0.499) GSTENP00037488001 (score: 0.122)	From Inparanoid:20070104
E. coli O157	PRPD	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)	PF03972 MmgE/PrpD family
Panther (EcoliWiki Page)	PTHR16943:SF7
Superfamily (EcoliWiki Page)	SUPERFAMILY:103378
EcoCyc	EcoCyc:G6199	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13603	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002816	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3371	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001152	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)
↑ ^2.00 ^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 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).

prpD:On One Page

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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 prpD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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