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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	sdaB
Gene Synonym(s)	ECK2792, b2797, JW2768^[1], JW2768
Product Desc.	LSERINEDEAM2^[2]^[3] L-Serine deaminase II; L-SD2^[4]
Product Synonyms(s)	L-serine deaminase II^[1], B2797^[2]^[1], SdaB^[2]^[1], L-threonine deaminase II^[2]^[1], L-serine deaminase 2^[2]^[1], L-serine dehydratase 2^[2]^[1], SDH-2^[2]^[1], L-SD2^[2]^[1], L-serine hydro-lyase 2 (deaminating)^[2]^[1] , ECK2792, JW2768, b2797
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): sdaCB^[2]
Regulation/Activity
Quick Links
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Notes

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Binds TrxA (Kumar, 2004).^[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	sdaB
Mnemonic	Serine deaminase
Synonyms	ECK2792, b2797, JW2768^[1], JW2768
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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	63.1 minutes	MG1655: 2927598..2928965 <gbrowseImage> name=NC_000913:2927598..2928965 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2818505..2819872 <gbrowseImage> name=NC_012967:2818505..2819872 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2814746..2816113 <gbrowseImage> name=NC_012759:2814746..2816113 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2928232..2929599 <gbrowseImage> name=NC_007779:2928232..2929599 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3021476..3022843 <gbrowseImage> name=NC_010473:3021476..3022843 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: Type	Phenotype: Description	Reference	Availability	Comments
ΔsdaB (Keio:JW2768)	deletion	deletion			PMID:16738554	Shigen CGSC10171^[5]
sdaB::Tn5KAN-I-SceI (FB20931)	Insertion at nt 894 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20931	contains pKD46
sdaB::Tn5KAN-I-SceI (FB20932)	Insertion at nt 894 in Plus orientation				PMID:15262929	E. coli Genome Project:FB20932	does not contain pKD46
ΔsdaB724::kan					PMID:16738554	CGSC:102888
sdaA(del) sdaB(del) tdcG(del)	deletion	deletion	Colony Morphology	When triple mutant is grown in liquid glucose minimal medium supplemented with casamino acids produced misshaped cells and eventually lysed, figure 2.	PMID:18532981	Parent Strain: MEW1 Experimental triple mutant strain: MEW999	Growth defect was due to the loss of L-serine deaminase and was proven by restoring wildtype growth even with casamino acids via strain with S-adenosylmethionine (SAM) plasmid insertion. MEW999psamT
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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
JW2768	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTAGCGTATTCGATATTTT Primer 2:CCATCGCAGGCAACGATCTTCAT
10B5	Kohara Phage	Genobase	PMID:3038334
8C5	Kohara Phage	Genobase	PMID:3038334
cysI95::Tn10	Linked marker	CAG12173 = CGSC7425^[5]	est. P1 cotransduction: 17% ^[6] Synonyms:cysC95::Tn10
fucP3072::Tn10	Linked marker	CAG12079 = CGSC7427^[5]	est. P1 cotransduction: 86% ^[6] Synonyms:fuc-3072::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:EG11623	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11623	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001571	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947262	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1580	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009172	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	SdaB
Synonyms	L-serine deaminase II^[1], B2797^[2]^[1], SdaB^[2]^[1], L-threonine deaminase II^[2]^[1], L-serine deaminase 2^[2]^[1], L-serine dehydratase 2^[2]^[1], SDH-2^[2]^[1], L-SD2^[2]^[1], L-serine hydro-lyase 2 (deaminating)^[2]^[1] , ECK2792, JW2768, b2797
Product description	LSERINEDEAM2^[2]^[3] L-Serine deaminase II; L-SD2^[4]
EC number (for enzymes)	4.3.1.17^[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:0003941	L-serine ammonia-lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004644	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003941	L-serine ammonia-lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005130	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003941	L-serine ammonia-lyase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005131	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003941	L-serine ammonia-lyase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.3.1.17	F	Seeded from EcoCyc (v14.0)	complete
	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:0006094	gluconeogenesis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004644	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006094	gluconeogenesis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005130	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006094	gluconeogenesis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005131	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006094	gluconeogenesis	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0312	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: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:0051539	4 iron, 4 sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005130	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005131	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0004	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	blc		PMID:16606699	Experiment(s):EBI-1143989
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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
Cytoplasm		PMID:8385012, PMID:8436113	EchoLocation:sdaB
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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 MISVFDIFKI GIGPSSSHTV GPMKAGKQFT DDLIARNLLK DVTRVVVDVY GSLSLTGKGH HTDIAIIMGL AGNLPDTVDI DSIPSFIQDV NTHGRLMLAN GQHEVEFPVD QCMNFHADNL SLHENGMRIT ALAGDKVVYS QTYYSIGGGF IVDEEHFGQQ DSAPVEVPYP YSSAADLQKH CQETGLSLSG LMMKNELALH SKEELEQHLA NVWEVMRGGI ERGISTEGVL PGKLRVPRRA AALRRMLVSQ DKTTTDPMAV VDWINMFALA VNEENAAGGR VVTAPTNGAC GIIPAVLAYY DKFIREVNAN SLARYLLVAS AIGSLYKMNA SISGAEVGCQ GEVGVACSMA AAGLAELLGA SPAQVCIAAE IAMEHNLGLT CDPVAGQVQV PCIERNAIAA VKAVNAARMA LRRTSEPRVC LDKVIETMYE TGKDMNAKYR ETSRGGLAMK IVACD
Length	455
Mol. Wt	48.752 kDa
pI	5.7 (calculated)
Extinction coefficient	28,880 - 30,130 (calc based on 12 Y, 2 W, and 10 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	182..450	PF03313 Serine dehydratase alpha chain	PMID:19920124
Domain	3..159	PF03315 Serine dehydratase beta chain	PMID:19920124
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<motif_map/>

Structure
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Structures

<beststructure> gene=sdaB 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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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:16130704	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947262	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009172	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P30744	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11623	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11623	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947262	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001571	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1580	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	4.88E+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	8533	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	80	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	1963	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)
sdaCB
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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_000913:2927578..2927618 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b2797 (EcoliWiki Page)	NCBI GEO profiles for sdaB
microarray	GenExpDB:b2797 (EcoliWiki Page)	Summary of data for sdaB 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 sdaB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11623	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1580	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2797
EcoGene	EcoGene:EG11623	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001571	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009172	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	ENSXETP00000020784 (score: 1.000; bootstrap: 100%) YP_026204 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	SDAB	From SHIGELLACYC
E. coli O157	SDAB	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:143548
Pfam (EcoliWiki Page)	PF03313 Serine dehydratase alpha chain
Pfam (EcoliWiki Page)	PF03315 Serine dehydratase beta chain
EcoCyc	EcoCyc:EG11623	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11623	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001571	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1580	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0009172	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 ^1.14 ^1.15 ^1.16 ^1.17 ^1.18 ^1.19 ^1.20 ^1.21 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 ^2.12 ^2.13 ^2.14 ^2.15 ^2.16 ^2.17 ^2.18 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).

sdaB: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 sdaB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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