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Gene |

Product(s) |

Expression|

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Standard Name	speD
Gene Synonym(s)	ECK0119, b0120, JW0116^[1], JW0116
Product Desc.	adenosylmethionine decarboxylase, proenzyme^[2]^[3] S-adenosylmethionine decarboxylase, spermidine biosynthesis; two subunits by cleavage: residues 1-111 are the beta chain and 112-264 are the alpha chain (153 aa)^[4]
Product Synonyms(s)	S-adenosylmethionine decarboxylase^[1], B0120^[2]^[1] , ECK0119, JW0116, b0120
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yacC-speED^[2]
Regulation/Activity
Quick Links
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Notes

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Paraquat toxicity observed in cells deficient in spermidine. The N-terminus of alpha chain, Ser112 is modified to pyrivic acid.^[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	speD
Mnemonic	Spermidine
Synonyms	ECK0119, b0120, JW0116^[1], JW0116
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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	2.91 minutes	MG1655: 135582..134788 <gbrowseImage> name=NC_000913:134788..135582 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 138385..137591 <gbrowseImage> name=NC_012967:137591..138385 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 134787..135581 <gbrowseImage> name=NC_012759:134787..135581 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 135582..134788 <gbrowseImage> name=NC_007779:134788..135582 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 109686..108892 <gbrowseImage> name=NC_010473:108892..109686 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	134788	Edman degradation	PMID:3546296
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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
speD(del) (Keio:JW0116)	deletion	deletion			PMID:16738554	[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen CGSC8398^[5]
speD98(del)					PMID:3526348	CGSC:6884
speD738(del)::kan					PMID:16738554	CGSC:102998
SMR4562 yiaG-yfp FRTcatFRT speD738(del)::FRTKanFRT	deletion		Sigma^S activity	Decrease in sigma^S activity	PMID:23224554	Parental Strain: SMR10582 Experimental Strain: SMR12828	See table S8 for full experimental results.
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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
JW0116	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAAAACTGAAACTGCATGG Primer 2:CCAACAGCTGGCATATTGCGCCC
4E11	Kohara Phage	Genobase	PMID:3038334
17C11	Kohara Phage	Genobase	PMID:3038334
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 9% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 62% ^[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:EG10962	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10962	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947719	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000951	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0955	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000416	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	SpeD
Synonyms	S-adenosylmethionine decarboxylase^[1], B0120^[2]^[1] , ECK0119, JW0116, b0120
Product description	adenosylmethionine decarboxylase, proenzyme^[2]^[3] S-adenosylmethionine decarboxylase, spermidine biosynthesis; two subunits by cleavage: residues 1-111 are the beta chain and 112-264 are the alpha chain (153 aa)^[4]
EC number (for enzymes)	4.1.1.50^[1]
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Notes

Function

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<protect> Gene Ontology

adenosylmethionine decarboxylase, proenzyme

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:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004014	adenosylmethionine decarboxylase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00465	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004014	adenosylmethionine decarboxylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003826	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004014	adenosylmethionine decarboxylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009165	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004014	adenosylmethionine decarboxylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004014	adenosylmethionine decarboxylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.1.50	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006557	S-adenosylmethioninamine biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00465	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006596	polyamine biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00465	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006596	polyamine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0620	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008295	spermidine biosynthetic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00465	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008295	spermidine biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003826	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008295	spermidine biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009165	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008295	spermidine biosynthetic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016067	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008295	spermidine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0745	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: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
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Interactions

adenosylmethionine decarboxylase, proenzyme

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 adenosylmethionine decarboxylase, β complex	could be indirect
Protein	ftsB		PMID:16606699	Experiment(s):EBI-1135640
Protein	dnaK		PMID:16606699	Experiment(s):EBI-1135640
Protein	sucA		PMID:19402753	LCMS(ID Probability):99.6
Protein	sucB		PMID:19402753	LCMS(ID Probability):99.6
Protein	Subunits of adenosylmethionine decarboxylase	could be indirect
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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 MKKLKLHGFN NLTKSLSFCI YDICYAKTAE ERDGYIAYID ELYNANRLTE ILSETCSIIG ANILNIARQD YEPQGASVTI LVSEEPVDPK LIDKTEHPGP LPETVVAHLD KSHICVHTYP ESHPEGGLCT FRADIEVSTC GVISPLKALN YLIHQLESDI VTIDYRVRGF TRDINGMKHF IDHEINSIQN FMSDDMKALY DMVDVNVYQE NIFHTKMLLK EFDLKHYMFH TKPEDLTDSE RQEITAALWK EMREIYYGRN MPAV
Length	264
Mol. Wt	30.385 kDa
pI	5.2 (calculated)
Extinction coefficient	26,360 - 27,110 (calc based on 14 Y, 1 W, and 6 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	32..169	PF02675 S-adenosylmethionine 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=speD taxon=562,83333 </beststructure>

Models

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Structure figures

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Notes

Gene Product Resources

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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:16128113	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947719	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000416	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7F6	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10962	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10962	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947719	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000951	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0955	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 MC4100	7.27E+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	Ecoli K-12	48.701+/-0.446	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.073047859	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	6346	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	1745	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	1826	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)
yacC-speED
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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_000913:135562..135602 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:b0120 (EcoliWiki Page)	NCBI GEO profiles for speD
microarray	GenExpDB:b0120 (EcoliWiki Page)	Summary of data for speD 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 speD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10962	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0955	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0120
EcoGene	EcoGene:EG10962	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000951	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000416	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
Shigella flexneri	SPED	From SHIGELLACYC
E. coli O157	SPED	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)	PF02675 S-adenosylmethionine decarboxylase
Superfamily (EcoliWiki Page)	SUPERFAMILY:56276
EcoCyc	EcoCyc:EG10962	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10962	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000951	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0955	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000416	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 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).

speD: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

adenosylmethionine decarboxylase, proenzyme

adenosylmethionine decarboxylase, proenzyme

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 speD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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