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Gene |

Product(s) |

Expression|

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Standard Name	hsdS
Gene Synonym(s)	ECK4338, b4348, JW4311, hss, hsp, rm^[1]^[2]
Product Desc.	specificity determinant for hsdM and hsdR^[2]^[3]; Component of [[:Category:Complex:EcoKI restriction-modification system\|EcoKI restriction-modification system]]^[3] Specificity determinant for HsdM and HsdR^[4]
Product Synonyms(s)	specificity determinant for hsdM and hsdR^[1], B4348^[2]^[1], Hss^[2]^[1], Hsp^[2]^[1], HsdS^[2]^[1] , ECK4338, hsp, hss, JW4311, b4348
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hsdMS^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

The restriction-modification complex EcoKI is comprised of three polypeptide subunits coded for by the genes hsdS, hsdM, and hsdR. HsdS is the polypeptide that directly interacts with DNA through the use of two target recognition domain (TRD) sequences first isolated by Fuller-Pace and Murray.^[5] HsdS recognizes and binds to the nucleotide sequence 5' AAC(N)₆GTGC. Fuller-Pace and Murray determined this sequence of the TRDs in hsdS after recombining two homologous hsdS genes from a family of restriction-modification complexes.

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Substitution of Trp212 to Arg alters the protein-protein interaction with HsdM, in turn effecting the DNA binding of the molecule; DNA binding in the mutant is restored by HsdR binding.^[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	hsdS
Mnemonic	Host specificity
Synonyms	ECK4338, b4348, JW4311, hss, hsp, rm^[1]^[2]
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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	98.67 minutes	MG1655: 4579485..4578091 <gbrowseImage> name=NC_000913:4578091..4579485 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4559437..4558013 <gbrowseImage> name=NC_012967:4558013..4559437 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4516575..4517969 <gbrowseImage> name=NC_012759:4516575..4517969 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4586142..4584748 <gbrowseImage> name=NC_007779:4584748..4586142 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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	Comments
ΔhsdS (Keio:JW4311)	deletion	deletion	PMID:16738554	Shigen CGSC11081^[6]
hsdS1				CGSC:7765
hsdS918				CGSC:10074
hsdS3				CGSC:10079
hsdS10				CGSC:10088
hsdS14				CGSC:12115
hsdS21				CGSC:12909
hsdS412				CGSC:14512
hsdS12				CGSC:14533
[hsdS20]				CGSC:37776	null allele
ΔhsdS746::kan			PMID:16738554	CGSC:101418
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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
JW4311	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGTGCGGGGAAATTGCCGGA Primer 2:CCGGATTTTTTACGTGAGGCTTT
12G5	Kohara Phage	Genobase	PMID:3038334
10H12	Kohara Phage	Genobase	PMID:3038334
zjf-920::Tn10	Linked marker	CAG12019 = CGSC7484^[6]	est. P1 cotransduction: % ^[7] Synonyms:zjh-901::Tn10, zjg-920::Tn10
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[6]	est. P1 cotransduction: 58% ^[7] Synonyms:zjj-202::Tn10, zji-202::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:EG10460	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10460	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000453	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948867	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0455	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014258	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	HsdS
Synonyms	specificity determinant for hsdM and hsdR^[1], B4348^[2]^[1], Hss^[2]^[1], Hsp^[2]^[1], HsdS^[2]^[1] , ECK4338, hsp, hss, JW4311, b4348
Product description	specificity determinant for hsdM and hsdR^[2]^[3]; Component of [[:Category:Complex:EcoKI restriction-modification system\|EcoKI restriction-modification system]]^[3] Specificity determinant for HsdM and HsdR^[4]
EC number (for enzymes)
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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:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000055	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006304	DNA modification	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000055	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009307	DNA restriction-modification system	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0680	P	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 [[:Category:Complex:EcoKI restriction-modification system\|EcoKI restriction-modification system]]	could be indirect
Protein	aceF		PMID:15690043	Experiment(s):EBI-890261, EBI-895222
Protein	hsdM		PMID:15690043	Experiment(s):EBI-890261, EBI-895222
Protein	hsdR		PMID:15690043	Experiment(s):EBI-895222
Protein	hupA		PMID:15690043	Experiment(s):EBI-895222
Protein	hupB		PMID:15690043	Experiment(s):EBI-895222
Protein	lpdA		PMID:15690043	Experiment(s):EBI-895222
Protein	malP		PMID:15690043	Experiment(s):EBI-895222
Protein	rplD		PMID:15690043	Experiment(s):EBI-895222
Protein	rplU		PMID:15690043	Experiment(s):EBI-895222
Protein	rpsG		PMID:15690043	Experiment(s):EBI-895222
Protein	hflB		PMID:16606699	Experiment(s):EBI-1147886
Protein	rplU		PMID:19402753	LCMS(ID Probability):99.6
Protein	rplD		PMID:19402753	LCMS(ID Probability):99.6
Protein	hsdM		PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):28.692887
Protein	hsdR		PMID:19402753	LCMS(ID Probability):99.6
Protein	hupA		PMID:19402753	LCMS(ID Probability):99.6
Protein	malP		PMID:19402753	LCMS(ID Probability):99.6
Protein	hupB		PMID:19402753	LCMS(ID Probability):99.6
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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
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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 MSAGKLPEGW VIAPVSTVTT LIRGVTYKKE QAINYLKDDY LPLIRANNIQ NGKFDTTDLV FVPKNLVKES QKISPEDIVI AMSSGSKSVV GKSAHQHLPF ECSFGAFCGV LRPEKLIFSG FIAHFTKSSL YRNKISSLSA GANINNIKPA SFDLINIPIP PLAEQKIIAE KLDTLLAQVD STKARFEQIP QILKRFRQAV LGGAVNGKLT EKWRNFEPQH SVFKKLNFES ILTELRNGLS SKPNESGVGH PILRISSVRA GHVDQNDIRF LECSESELNR HKLQDGDLLF TRYNGSLEFV GVCGLLKKLQ HQNLLYPDKL IRARLTKDAL PEYIEIFFSS PSARNAMMNC VKTTSGQKGI SGKDIKSQVV LLPPVKEQAE IVRRVEQLFA YADTIEKQVN NALARVNNLT QSILAKAFRG ELTAQWRAEN PDLISGENSA AALLEKIKAE RAASGGKKAS RKKS
Length	464
Mol. Wt	51.396 kDa
pI	10.0 (calculated)
Extinction coefficient	28,420 - 29,045 (calc based on 8 Y, 3 W, and 5 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	7..191	PF01420 Type I restriction modification DNA specificity domain	PMID:19920124
Domain	318..405	PF01420 Type I restriction modification DNA specificity 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=hsdS 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:16132169	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948867	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014258	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P05719	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10460	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10460	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948867	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000453	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0455	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	2.123+/-0.032	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.013629842	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	552	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	158	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	212	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)
hsdMS
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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_000913:4579465..4579505 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:b4348 (EcoliWiki Page)	NCBI GEO profiles for hsdS
microarray	GenExpDB:b4348 (EcoliWiki Page)	Summary of data for hsdS 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 hsdS Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10460	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0455	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4348
EcoGene	EcoGene:EG10460	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000453	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014258	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	ENSANGP00000029253 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	Z5946	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)	PF01420 Type I restriction modification DNA specificity domain
Pfam (EcoliWiki Page)	PF01420 Type I restriction modification DNA specificity domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:116734
Superfamily (EcoliWiki Page)	SUPERFAMILY:116734
EcoCyc	EcoCyc:EG10460	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10460	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000453	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0455	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014258	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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 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 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Fuller-Pace, FV & Murray, NE (1986) Two DNA recognition domains of the specificity polypeptides of a family of type I restriction enzymes. Proc. Natl. Acad. Sci. U.S.A. 83 9368-72 PubMed
↑ ^6.0 ^6.1 ^6.2 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 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).

hsdS: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 hsdS Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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