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Gene Name

hsdS (synonyms: ECK4338, b4348, JW4311, hss, hsp, rm)[1][2]

Product(s)

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

Description

specificity determinant for hsdM and hsdR[2][3]

Component of EcoKI restriction-modification system[3]

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hsdMS[2]

Regulation/Activity
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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.[4] 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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Gene

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Nomenclature

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Standard name

hsdS

Mnemonic
Synonyms

ECK4338, b4348, JW4311, hss, hsp, rm[1][2]

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Notes

Location(s) and DNA Sequence

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StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

98.67 minutes 

MG1655: 4579485..4578091
gbrowse_img.php?coord=4577091..4580485&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 4586142..4584748
gbrowse_img.php?coord=4583748..4587142&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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Notes

Sequence Features

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Feature typeLocationDescription
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Notes

Alleles and Phenotypes

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

ΔhsdS (Keio:JW4311)

deletion

deletion

PMID:16738554[5]

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[5]

CGSC:101418


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Notes

Genetic Resources

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ResourceResource TypeSourceNotes/Reference

JW4311

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAGTGCGGGGAAATTGCCGGA

Primer 2:CCGGATTTTTTACGTGAGGCTTT

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[6]

est. P1 cotransduction: % [8]

Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[6]

est. P1 cotransduction: 58% [8]

Synonyms:zjj-202::Tn10, zji-202::Tn10

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Notes

Accessions in Other Databases

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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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NameURLComments
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Categories

Product(s)

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Nomenclature

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]

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[9]

IPI: Inferred from Physical Interaction

UniProtKB:P0AAI3

F

Seeded from EcoCyc 12.5 [10]

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 12.5 [10]

complete

GO:0006304

DNA modification

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000055

P

Seeded from EcoCyc 12.5 [10]

complete

GO:0009307

DNA restriction-modification system

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0680

P

Seeded from EcoCyc 12.5 [10]

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

Partner TypePartnerNotesReferences

Protein

Subunits of [[:Category:Complex:EcoKI restriction-modification system|EcoKI restriction-modification system]]

could be indirect


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Notes

Localization

CompartmentDescriptionEvidenceNotes
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Notes

Structure and Physical Properties

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Physical Properties

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
Mol. Wt

51.4 kDa (calc) [2]

pI
Extinction coefficient

28420 - 29045 (calc based on 8 Y, 3 W, and 5 C residues)

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Domains/Motifs/Modification Sites

TypeResiduesDescriptionNotes
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Structure

Structures
  • Representative homolog:
    1YF2|A (Methanocaldococcus jannaschii )
    14-232 of 464 residues (E-value: 5.4e-09) (Percent Identity: 23.89)
  • View all other structures.
Models

View models at:

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Notes

Gene Product Resources

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Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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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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NameURLComments
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Categories

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[[Category:Complex:EcoKI restriction-modification system]]

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.

Transcription and Transcriptional Regulation

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Transcription unit(s)

hsdMS

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Figure courtesy of RegulonDB
Figure courtesy of RegulonDB

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

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=Genes_unlabeled+DNA_unlabeled+flip&width=400&.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

Allele NameMutationPhenotypeReference
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Expression Studies

TypeReferenceNotes

microarray

EcoliGenExpDB:b4348 (EcoliWiki Page)

Summary of data for hsdS from multiple microarray studies

microarray

GEO Profiles:b4348 (EcoliWiki Page)

NCBI GEO profiles for hsdS

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Expression Resources

Resource NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to hsdS Expression

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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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NameURLComments
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Categories

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Evolution

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Homologs in Other Organisms

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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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NameURLComments
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References

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

  1. ↑ 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. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 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. ↑ 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
  5. ↑ 5.0 5.1 Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
  6. ↑ 6.0 6.1 6.2 CGSC: The Coli Genetics Stock Center
  7. ↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
  8. ↑ 8.0 8.1 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).
  9. ↑ Arifuzzaman M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16: 686-91 PubMed EcoliWiki page
  10. ↑ 10.0 10.1 10.2 10.3 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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