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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	ppiD
Gene Synonym(s)	ECK0435, b0441, JW0431, ybaU^[1], ybaU
Product Desc.	G6242^[2]^[3] Peptidylprolyl-cis-trans-isomerase D, rotamase; involved in the folding of outer membrane proteins^[4]
Product Synonyms(s)	peptidyl-prolyl cis-trans isomerase (rotamase D)^[1], B0441^[2]^[1], YbaU^[2]^[1], PpiD^[2]^[1] , ECK0435, JW0431, ybaU, b0441
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ppiD^[2]
Regulation/Activity
Quick Links
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Notes

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PpiD is a periplasmic enyzyme with N-terminal membrane anchor. Heat-inducible. An fkpA, surA, ppiB, ppiD quadruple mutant is viable.^[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	ppiD
Mnemonic	Peptidylprolyl isomerase
Synonyms	ECK0435, b0441, JW0431, ybaU^[1], ybaU
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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	9.94 minutes	MG1655: 461139..463010 <gbrowseImage> name=NC_000913:461139..463010 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 433970..435841 <gbrowseImage> name=NC_012967:433970..435841 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 363898..365769 <gbrowseImage> name=NC_012759:363898..365769 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 461139..463010 <gbrowseImage> name=NC_007779:461139..463010 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 400470..402341 <gbrowseImage> name=NC_010473:400470..402341 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: Description	Reference	Availability	Comments
ΔppiD (Keio:JW0431)	deletion	deletion		PMID:16738554	Shigen CGSC8594^[5]
ppiDG312A,R		G312A,R	Loss of activity			seeded from UniProt:P0ADY1
ppiDG313A,R		G313A,R	Loss of activity			seeded from UniProt:P0ADY1
ppiDG347A		G347A	Loss of activity			seeded from UniProt:P0ADY1
ppiDI350A,F		I350A,F	Loss of activity			seeded from UniProt:P0ADY1
zaj-3054::Tn10	Insertion at 461,486 bp in MG1655 (NC_000913)			adapted from Nichols et al.^[6]	CAG12017 = CGSC7339^[5]	Synonyms: zba-3054::Tn10
ΔppiD727::kan				PMID:16738554	CGSC:102434
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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
JW0431	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATGGACAGCTTACGCACGGC Primer 2:CCTTGCTGTTCCAGCGCATCGCC
3B6	Kohara Phage	Genobase	PMID:3038334
7E2	Kohara Phage	Genobase	PMID:3038334
tsx-247::Tn10	Linked marker	CAG12148 = CGSC7337^[5]	est. P1 cotransduction: 32% ^[6]
gsk-3055::Tn10	Linked marker	CAG12154 = CGSC7341^[5]	est. P1 cotransduction: 18% ^[6] Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
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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:G6242	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13249	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002853	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946056	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3038	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001531	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	PpiD
Synonyms	peptidyl-prolyl cis-trans isomerase (rotamase D)^[1], B0441^[2]^[1], YbaU^[2]^[1], PpiD^[2]^[1] , ECK0435, JW0431, ybaU, b0441
Product description	G6242^[2]^[3] Peptidylprolyl-cis-trans-isomerase D, rotamase; involved in the folding of outer membrane proteins^[4]
EC number (for enzymes)	5.2.1.8^[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:0031225	anchored to membrane				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.2.1.8	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003755	peptidyl-prolyl cis-trans isomerase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0697	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006457	protein folding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0697	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006950	response to stress	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0346	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016853	isomerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000297	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016853	isomerase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0413	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	sucB	PMID:16606699	Experiment(s):EBI-1136695
Protein	puuB	PMID:16606699	Experiment(s):EBI-1136695
Protein	glpD	PMID:16606699	Experiment(s):EBI-1136695
Protein	dnaE	PMID:16606699	Experiment(s):EBI-1136695
Protein	zwf	PMID:16606699	Experiment(s):EBI-1136695
Protein	yfgM	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):26.888575
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Notes

Localization

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

Compartment	Evidence	Reference/Source
plasma membrane		From EcoCyc^[3]
Inner Membrane	PMID:9670013, PMID:16079137, PMID:9670013	EchoLocation:ppiD
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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 MMDSLRTAAN SLVLKIIFGI IIVSFILTGV SGYLIGGGNN YAAKVNDQEI SRGQFENAFN SERNRMQQQL GDQYSELAAN EGYMKTLRQQ VLNRLIDEAL LDQYARELKL GISDEQVKQA IFATPAFQVD GKFDNSRYNG ILNQMGMTAD QYAQALRNQL TTQQLINGVA GTDFMLKGET DELAALVAQQ RVVREATIDV NALAAKQPVT EQEIASYYEQ NKNNFMTPEQ FRVSYIKLDA ATMQQPVSDA DIQSYYDQHQ DQFTQPQRTR YSIIQTKTED EAKAVLDELN KGGDFAALAK EKSADIISAR NGGDMGWLED ATIPDELKNA GLKEKGQLSG VIKSSVGFLI VRLDDIQPAK VKSLDEVRDD IAAKVKHEKA LDAYYALQQK VSDAASNDTE SLAGAEQAAG VKATQTGWFS KDNLPEELNF KPVADAIFNG GLVGENGAPG INSDIITVDG DRAFVLRISE HKPEAVKPLA DVQEQVKALV QHNKAEQQAK VDAEKLLVDL KAGKGAEAMQ AAGLKFGEPK TLSRSGRDPI SQAAFALPLP AKDKPSYGMA TDMQGNVVLL ALDEVKQGSM PEDQKKAMVQ GITQNNAQIV FEALMSNLRK EAKIKIGDAL EQQ
Length	623
Mol. Wt	68.15 kDa
pI	4.8 (calculated)
Extinction coefficient	34,840 (calc based on 16 Y, 2 W, and 0 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	References
Domain	258..355	PF00639 PPIC-type PPIASE domain	PMID:19920124
Domain	41..166	PF09312 SurA N-terminal domain	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=ppiD 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:16128426	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946056	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001531	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ADY1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6242	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13249	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946056	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002853	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3038	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	6.86E+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	3717	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	666	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	1644	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)
ppiD
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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_000913:461119..461159 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:b0441 (EcoliWiki Page)	NCBI GEO profiles for ppiD
microarray	GenExpDB:b0441 (EcoliWiki Page)	Summary of data for ppiD 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 (460861..461145) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:G6^[7]
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Notes

Accessions Related to ppiD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6242	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3038	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0441
EcoGene	EcoGene:EG13249	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002853	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001531	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
Xenopus tropicalis	ENSXETP00000031299 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YBAU	From SHIGELLACYC
E. coli O157	YBAU	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:54534
Superfamily (EcoliWiki Page)	SUPERFAMILY:109998
Pfam (EcoliWiki Page)	PF00639 PPIC-type PPIASE domain
Pfam (EcoliWiki Page)	PF09312 SurA N-terminal domain
EcoCyc	EcoCyc:G6242	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13249	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002853	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3038	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001531	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 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 ^3.2 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 ^5.3 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 ^6.2 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

ppiD: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 ppiD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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