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hsdS:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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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 product[1], B4348 product[2][1], Hss product[2][1], Hsp product[2][1], HsdS product[2][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hsdMS[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(hsdS)    Textpresso(hsdS)

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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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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

98.67 minutes 

MG1655: 4579485..4578091
gbrowse_img.php?coord=4578091..4579485&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4559437..4558013
gbrowse_img.php?coord=4558013..4559437&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4586142..4584748
gbrowse_img.php?coord=4584748..4586142&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 4516575..4517969
gbrowse_img.php?coord=4516575..4517969&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

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 Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW4311

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGTGCGGGGAAATTGCCGGA

Primer 2:CCGGATTTTTTACGTGAGGCTTT

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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10460

EchoBASE (EcoliWiki Page)

EchoBASE:EB0455

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4348

EcoGene (EcoliWiki Page)

EcoGene:EG10460

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z5946

CGSC (EcoliWiki Page)

CGSC:619

ASAP (EcoliWikiPage)

ASAP:ABE-0014258


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Notes

Links

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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 product

Synonyms

specificity determinant for hsdM and hsdR product[1], B4348 product[2][1], Hss product[2][1], Hsp product[2][1], HsdS product[2][1]

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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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0005515

protein binding

PMID:16606699

IPI: Inferred from Physical Interaction

UniProtKB:P0AAI3

F

Seeded from EcoCyc [8]

complete

GO:0003677

DNA binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR000055
SP_KW:KW-0238

F

Seeded from EcoCyc [8]

complete

GO:0006304

DNA modification

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000055

P

Seeded from EcoCyc [8]

complete

GO:0009307

DNA restriction-modification system

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0680

P

Seeded from EcoCyc [8]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0006306

DNA methylation

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

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

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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.

TypeResiduesDescriptionNotesReferences
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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10460-MONOMER

UniProt (EcoliWiki Page)

UniProt:P05719

PFAM (EcoliWiki Page)

PFAM:PF01420

RefSeq (EcoliWiki Page)

RefSeq:NP_418768

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z5946-MONOMER


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Notes

Links

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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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

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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gbrowse_img.php?coord=4579465..4579505&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

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 NameResource TypeDescriptionSourceNotes
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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10460

EchoBASE (EcoliWiki Page)

EchoBASE:EB0455

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4348

EcoGene (EcoliWiki Page)

EcoGene:EG10460


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Notes

Links

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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.

OrganismHomologs (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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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF01420


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 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. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 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 EcoliWiki page
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ 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).
  8. ↑ 8.0 8.1 8.2 8.3 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70

Categories

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