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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	lysA
Gene Synonym(s)	ECK2836, b2838, JW2806^[1], JW2806
Product Desc.	LysA^[2]^[3]; Component of diaminopimelate decarboxylase^[2]^[3] Diaminopimelate decarboxylase^[4]
Product Synonyms(s)	diaminopimelate decarboxylase, PLP-binding^[1], B2838^[2]^[1], LysA^[2]^[1] , ECK2836, JW2806, b2838
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): lysA^[2], OP00257
Regulation/Activity
Quick Links
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Notes

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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	lysA
Mnemonic	Lysine
Synonyms	ECK2836, b2838, JW2806^[1], JW2806
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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	64.14 minutes	MG1655: 2976921..2975659 <gbrowseImage> name=NC_000913:2975659..2976921 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2873520..2872258 <gbrowseImage> name=NC_012967:2872258..2873520 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2862807..2864069 <gbrowseImage> name=NC_012759:2862807..2864069 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2977555..2976293 <gbrowseImage> name=NC_007779:2976293..2977555 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3070791..3069529 <gbrowseImage> name=NC_010473:3069529..3070791 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)	Reference	Availability
ΔlysA (Keio:JW2806)	deletion	deletion	PMID:16738554	Shigen CGSC10193^[5]
lysA23				CGSC:5087
lysA29				CGSC:5241
lysA22				CGSC:6775
lysA24				CGSC:9365
lysA0::Tn10				CGSC:10967
lysA27::Mu				CGSC:11575
lysA35				CGSC:12208
lysA28				CGSC:14251
lysA25				CGSC:72557
ΔlysA763::kan			PMID:16738554	CGSC:101706
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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
JW2806	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCCACATTCACTGTTCAGCAC Primer 2:CCAAGCAATTCCAGCGCCAGTAA
8H3	Kohara Phage	Genobase	PMID:3038334
12H3	Kohara Phage	Genobase	PMID:3038334
recD1901::Tn10	Linked marker	CAG12135 = CGSC7429^[5]	est. P1 cotransduction: 39% ^[6]
speA210::Tn10	Linked marker	CAG12168 = CGSC7431^[5]	est. P1 cotransduction: % ^[6] Synonyms:zgd-210::Tn10, zgf-210::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:EG10549	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10549	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000542	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947313	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0544	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009309	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	LysA
Synonyms	diaminopimelate decarboxylase, PLP-binding^[1], B2838^[2]^[1], LysA^[2]^[1] , ECK2836, JW2806, b2838
Product description	LysA^[2]^[3]; Component of diaminopimelate decarboxylase^[2]^[3] Diaminopimelate decarboxylase^[4]
EC number (for enzymes)	4.1.1.20^[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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000183	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009006	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008652	cellular amino acid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0028	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008836	diaminopimelate decarboxylase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002986	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008836	diaminopimelate decarboxylase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.1.1.20	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009085	lysine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0457	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009089	lysine biosynthetic process via diaminopimelate	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002986	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 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 diaminopimelate decarboxylase	could be indirect
Protein	frvX		PMID:16606699	Experiment(s):EBI-1144123
Protein	lldR		PMID:16606699	Experiment(s):EBI-1144123
Protein	pgsA		PMID:16606699	Experiment(s):EBI-1144123
Protein	greA		PMID:16606699	Experiment(s):EBI-1144123
Protein	cpxR		PMID:15690043	Experiment(s):EBI-895120
Protein	cpxR		PMID:19402753	LCMS(ID Probability):99.4
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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 MPHSLFSTDT DLTAENLLRL PAEFGCPVWV YDAQIIRRQI AALKQFDVVR FAQKACSNIH ILRLMREQGV KVDSVSLGEI ERALAAGYNP QTHPDDIVFT ADVIDQATLE RVSELQIPVN AGSVDMLDQL GQVSPGHRVW LRVNPGFGHG HSQKTNTGGE NSKHGIWYTD LPAALDVIQR HHLQLVGIHM HIGSGVDYAH LEQVCGAMVR QVIEFGQDLQ AISAGGGLSV PYQQGEEAVD TEHYYGLWNA AREQIARHLG HPVKLEIEPG RFLVAQSGVL ITQVRSVKQM GSRHFVLVDA GFNDLMRPAM YGSYHHISAL AADGRSLEHA PTVETVVAGP LCESGDVFTQ QEGGNVETRA LPEVKAGDYL VLHDTGAYGA SMSSNYNSRP LLPEVLFDNG QARLIRRRQT IEELLALELL
Length	420
Mol. Wt	46.176 kDa
pI	6.0 (calculated)
Extinction coefficient	39,880 - 40,380 (calc based on 12 Y, 4 W, and 4 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	32..276	PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain	PMID:19920124
Domain	279..397	PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet 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=lysA 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:16130742	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009309	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P00861	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10549	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10549	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947313	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000542	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947313	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0544	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	Ecoli K-12	11.292+/-0.101	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.011093502	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	1317	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	726	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	2418	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)
lysA
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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_000913:2976901..2976941 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:b2838 (EcoliWiki Page)	NCBI GEO profiles for lysA
microarray	GenExpDB:b2838 (EcoliWiki Page)	Summary of data for lysA 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 (2976849..2977099) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:D2^[7]
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Notes

Accessions Related to lysA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10549	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0544	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2838
EcoGene	EcoGene:EG10549	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000542	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009309	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	ENSANGP00000008816 (score: 1.000; bootstrap: 100%) ENSANGP00000009019 (score: 0.426) ENSANGP00000020224 (score: 0.423) ENSANGP00000008815 (score: 0.317) ENSANGP00000020301 (score: 0.171)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G14390 (score: 1.000; bootstrap: 100%) AT5G11880 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00038323 (score: 1.000; bootstrap: 100%) WBGene00033029 (score: 0.106)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00003844 (score: 1.000; bootstrap: 100%) WBGene00018764 (score: 0.107)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000007432 (score: 1.000; bootstrap: 100%) ENSCINP00000008768 (score: 0.181)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0190621 (score: 1.000; bootstrap: 77%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0013307 (score: 1.000; bootstrap: 100%) FBgn0013308 (score: 0.727)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000021660 (score: 1.000; bootstrap: 100%) ENSMODP00000018485 (score: 0.511) ENSMODP00000007263 (score: 0.358)	From Inparanoid:20070104
Mus musculus	MGI:1859169 (score: 1.000; bootstrap: 100%) MGI:97402 (score: 0.437) MGI:2442093 (score: 0.363)	From Inparanoid:20070104
Oryza gramene	Q6ZG77 (score: 1.000; bootstrap: 96%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000031505 (score: 1.000; bootstrap: 100%) ENSRNOP00000007259 (score: 0.421) ENSRNOP00000007999 (score: 0.316) ENSRNOP00000045880 (score: 0.194) ENSRNOP00000049464 (score: 0.169) ENSRNOP00000039827 (score: 0.131) ENSRNOP00000043900 (score: 0.124) ENSRNOP00000037115 (score: 0.083)	From Inparanoid:20070104
Saccharomyces cerevisiae	YKL184W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC1444c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000156319 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000137759 (score: 0.389) NEWSINFRUP00000147907 (score: 0.277) NEWSINFRUP00000147578 (score: 0.219) NEWSINFRUP00000168901 (score: 0.177)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000020790 (score: 1.000; bootstrap: 97%)	From Inparanoid:20070104
Shigella flexneri	LYSA	From SHIGELLACYC
E. coli O157	LYSA	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)	PF00278 Pyridoxal-dependent decarboxylase, C-terminal sheet domain
Pfam (EcoliWiki Page)	PF02784 Pyridoxal-dependent decarboxylase, pyridoxal binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:50621
Superfamily (EcoliWiki Page)	SUPERFAMILY:51419
Panther (EcoliWiki Page)	PTHR11482:SF35
EcoCyc	EcoCyc:EG10549	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10549	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000542	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0544	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009309	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 ^1.8 ^1.9 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 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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

lysA: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 lysA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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