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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	psd
Gene Synonym(s)	ECK4156, b4160, JW4121^[1], JW4121
Product Desc.	phosphatidylserine decarboxylase, proenzyme^[2]^[3] phosphatidylserine decarboxylase, β subunit^[2]^[3] Phosphatidylserine decarboxylase; phospholipid biosynthesis; residues 1-253 cleaved constituting beta chain; N-terminal (69aa) constitutes the alpha chain^[4]
Product Synonyms(s)	phosphatidylserine decarboxylase^[1], B4160^[2]^[1] , ECK4156, JW4121, b4160
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yjeP^[2], psd^[2]
Regulation/Activity
Quick Links
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Notes

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N-terminal of alpha subunit (Ser254) is midified to pyruvic acid, a point mutation here results in reduced processing.^[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	psd
Mnemonic	Phosphatidylserine decarboxylase
Synonyms	ECK4156, b4160, JW4121^[1], JW4121
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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	94.56 minutes	MG1655: 4388383..4387415 <gbrowseImage> name=NC_000913:4387415..4388383 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4368515..4367547 <gbrowseImage> name=NC_012967:4367547..4368515 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4326150..4327118 <gbrowseImage> name=NC_012759:4326150..4327118 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4395040..4394072 <gbrowseImage> name=NC_007779:4394072..4395040 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4488745..4487777 <gbrowseImage> name=NC_010473:4487777..4488745 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
Coding Start (SO:0000323)	MG1655	4387415	Edman degradation	PMID:3042771
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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	AA change(s)	Phenotype: Description	Availability	Comments
psdS254A	S254A	No processing of the proenzyme, complete loss of activity		seeded from UniProt:P0A8K1
psdS254C	S254C	Reduced processing, 16% wild-type activity		seeded from UniProt:P0A8K1
psdS254T	S254T	Reduced processing, 2% wild-type activity		seeded from UniProt:P0A8K1
psd-2(ts)		temperature sensitive	CGSC:8626
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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
JW4121	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTAAATTCATTTAAACTTTC Primer 2:CCGACCTGGTCTTTTTTGTCGTC
3H6	Kohara Phage	Genobase	PMID:3038334
3A1	Kohara Phage	Genobase	PMID:3038334
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 30% ^[6] Synonyms:zjd-2231::Tn10
cycA30::Tn10	Linked marker	CAG12073 = CGSC7482^[5]	est. P1 cotransduction: 20% ^[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:EG10775	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10775	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000766	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948673	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0768	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013623	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	Psd
Synonyms	phosphatidylserine decarboxylase^[1], B4160^[2]^[1] , ECK4156, JW4121, b4160
Product description	phosphatidylserine decarboxylase, proenzyme^[2]^[3] phosphatidylserine decarboxylase, β subunit^[2]^[3] Phosphatidylserine decarboxylase; phospholipid biosynthesis; residues 1-253 cleaved constituting beta chain; N-terminal (69aa) constitutes the alpha chain^[4]
EC number (for enzymes)	4.1.1.65^[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:0004609	phosphatidylserine decarboxylase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00662	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004609	phosphatidylserine decarboxylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003817	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004609	phosphatidylserine decarboxylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005221	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004609	phosphatidylserine decarboxylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.1.65	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-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008654	phospholipid biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00662	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008654	phospholipid biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003817	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008654	phospholipid biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005221	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008654	phospholipid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0594	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: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:0016831	carboxy-lyase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0210	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	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 phosphatidylserine decarboxylase, heterodimer	could be indirect
Protein	fur		PMID:16606699	Experiment(s):EBI-1147590
Protein	rplO		PMID:16606699	Experiment(s):EBI-1147590
Protein	Subunits of phosphatidylserine decarboxylase	could be indirect
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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
Cytoplasm	PMID:3042771, PMID:5543671	EchoLocation:psd
plasma membrane		From EcoCyc^[3]
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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 MLNSFKLSLQ YILPKLWLTR LAGWGASKRA GWLTKLVIDL FVKYYKVDMK EAQKPDTASY RTFNEFFVRP LRDEVRPIDT DPNVLVMPAD GVISQLGKIE EDKILQAKGH NYSLEALLAG NYLMADLFRN GTFVTTYLSP RDYHRVHMPC NGILREMIYV PGDLFSVNHL TAQNVPNLFA RNERVICLFD TEFGPMAQIL VGATIVGSIE TVWAGTITPP REGIIKRWTW PAGENDGSVA LLKGQEMGRF KLGSTVINLF APGKVNLVEQ LESLSVTKIG QPLAVSTETF VTPDAEPAPL PAEEIEAEHD ASPLVDDKKD QV
Length	322
Mol. Wt	35.934 kDa
pI	5.6 (calculated)
Extinction coefficient	46,410 - 46,660 (calc based on 9 Y, 6 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
Domain	63..285	PF02666 Phosphatidylserine decarboxylase		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=psd 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:16131985	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948673	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013623	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8K1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10775	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10775	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948673	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000766	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0768	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	3.39E+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	1980	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	486	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	828	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)
yjeP
psd
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Figure courtesy of RegulonDB

</protect>

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_000913:4388363..4388403 source=MG1655 flip=1 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:b4160 (EcoliWiki Page)	NCBI GEO profiles for psd
microarray	GenExpDB:b4160 (EcoliWiki Page)	Summary of data for psd 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 (4387845..4388117) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ09; Well:B11^[7]
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Notes

Accessions Related to psd Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10775	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0768	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4160
EcoGene	EcoGene:EG10775	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000766	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013623	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	ENSANGP00000013869 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000034982 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT4G25970 (score: 1.000; bootstrap: 54%) AT5G57190 (score: 0.860)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000011848 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00042321 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00015159 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000019491 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000000439 (score: 1.000; bootstrap: 100%) ENSCINP00000013641 (score: 0.204)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0204189 (score: 1.000; bootstrap: 56%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0026576 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA19281-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000011112 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000338695 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000002906 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000012210 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:2445114 (score: 1.000; bootstrap: 100%) MGI:3612472 (score: 0.227)	From Inparanoid:20070104
Oryza gramene	Q5JN42 (score: 1.000; bootstrap: 62%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000024593 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000024812 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNL169C (score: 1.000; bootstrap: 70%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC16E98 (score: 1.000; bootstrap: 77%) SPAC25B83 (score: 0.295)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000173513 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00024788001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000003317 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	PSD	From SHIGELLACYC
E. coli O157	Z5766	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)	PF02666 Phosphatidylserine decarboxylase
EcoCyc	EcoCyc:EG10775	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10775	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000766	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0768	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013623	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 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 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 ^3.4 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 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

psd: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 psd Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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