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hsdR:On One Page

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Standard Name

hsdR

Gene Synonym(s)

ECK4340, b4350, JW4313, Hs, hsp, hsr, rm[1]

Product Desc.

host restriction; endonuclease R[2][3];

Component of [[:Category:Complex:EcoKI restriction-modification system|EcoKI restriction-modification system]][3]

Endonuclease R, host restriction of foreign DNA; ClpXP-dependent degradation[4]

Product Synonyms(s)

endonuclease R product[1], B4350 product[2][1], Hsr product[2][1], Hsp product[2][1], HsdR product[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hsdRMS[3]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(hsdR)    Textpresso(hsdR)

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Notes

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HsdR acts as a chaperone in hsdS mutant to allow DNA 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

hsdR

Mnemonic

Host specificity

Synonyms

ECK4340, b4350, JW4313, Hs, hsp, hsr, rm[1]

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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

98.74 minutes 

MG1655: 4584838..4581272
gbrowse_img.php?coord=4581272..4584838&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4564736..4561224
gbrowse_img.php?coord=4561224..4564736&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4591495..4587929
gbrowse_img.php?coord=4587929..4591495&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 4519756..4523322
gbrowse_img.php?coord=4519756..4523322&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

ΔhsdR (Keio:JW4313)

deletion

deletion

PMID:16738554

Shigen
CGSC11083[5]

hsdRΔ4

deletion

deletion

Lacks DNA specifying six DEAD-box motifs that are critical for helicase activity

PMID: 9776741

hsdR514

CGSC:4539

hsdR2

CGSC:4558

hsdR4

CGSC:4756

hsdR17

CGSC:5437

hsdR19

CGSC:8723

hsdR0

CGSC:9056

ΔhsdR24

CGSC:9513

hsdR11

CGSC:10099

hsdR27

CGSC:10718

hsdR18

CGSC:12161

hsdR519

CGSC:14514

hsdR13

CGSC:14535

hsdR29

CGSC:28917

ΔhsdR748::kan

PMID:16738554

CGSC:101416


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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

JW4313

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTATGGGCgTTAAATATTTGGACAGGCCCG

Primer 2:CCGGCCAGCTCGTCCCAGATATA

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[5]

est. P1 cotransduction: % [6]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[5]

est. P1 cotransduction: 66% [6]
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:EG10459

EchoBASE (EcoliWiki Page)

EchoBASE:EB0454

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4350

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C5425

EcoGene (EcoliWiki Page)

EcoGene:EG10459

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z5948

CGSC (EcoliWiki Page)

CGSC:620

ASAP (EcoliWikiPage)

ASAP:ABE-0014264


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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

HsdR product

Synonyms

endonuclease R product[1], B4350 product[2][1], Hsr product[2][1], Hsp product[2][1], HsdR product[2][1]

Product description

host restriction; endonuclease R[2][3];

Component of [[:Category:Complex:EcoKI restriction-modification system|EcoKI restriction-modification system]][3]

Endonuclease R, host restriction of foreign DNA; ClpXP-dependent degradation[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:0000166

nucleotide binding

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc [7]

complete

GO:0003676

nucleic acid binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc [7]

complete

GO:0003677

DNA binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR006935
InterPro:IPR007409
SP_KW:KW-0238

F

Seeded from EcoCyc [7]

complete

GO:0004386

helicase activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc [7]

complete

GO:0004519

endonuclease activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007409

F

Seeded from EcoCyc [7]

complete

GO:0005524

ATP binding

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001650
InterPro:IPR006935
SP_KW:KW-0067

F

Seeded from EcoCyc [7]

complete

GO:0006304

DNA modification

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007409

P

Seeded from EcoCyc [7]

complete

GO:0009035

Type I site-specific deoxyribonuclease activity

GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.21.3

F

Seeded from EcoCyc [7]

complete

GO:0009307

DNA restriction-modification system

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0680

P

Seeded from EcoCyc [7]

complete

GO:0016787

hydrolase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR006935
SP_KW:KW-0378

F

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0006308

DNA catabolic process

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-889458, EBI-894477

Protein

hsdM

PMID:15690043

Experiment(s):EBI-889458, EBI-890115, EBI-894477, EBI-895107

Protein

lpdA

PMID:15690043

Experiment(s):EBI-889458, EBI-894477

Protein

rplL

PMID:15690043

Experiment(s):EBI-894477

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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 

MLWALNIWTG PHSNGLITMM NKSNFEFLKG VNDFTYAIAC AAENNYPDDP NTTLIKMRMF
GEATAKHLGL LLNIPPCENQ HDLLRELGKI AFVDDNILSV FHKLRRIGNQ AVHEYHNDLN
DAQMCLRLGF RLAVWYYRLV TKDYDFPVPV FVLPERGENL YHQEVLTLKQ QLEQQVREKA
QTQAEVEAQQ QKLVALNGYI AILEGKQQET EAQTQARLAA LEAQLAEKNA ELAKQTEQER
KAYHKEITDQ AIKRTLNLSE EESRFLIDAQ LRKAGWQADS KTLRFSKGAR PEPGVNKAIA
EWPTGKDETG NQGFADYVLF VGLKPIAVVE AKRNNIDVPA RLNESYRYSK CFDNGFLRET
LLEHYSPDEV HEAVPEYETS WQDTSGKQRF KIPFCYSTNG REYRATMKTK SGIWYRDVRD
TRNMSKALPE WHRPEELLEM LGSEPQKQNQ WFADNPGMSE LGLRYYQEDA VRAVEKAIVK
GQQEILLAMA TGTGKTRTAI AMMFRLIQSQ RFKRILFLVD RRSLGEQALG AFEDTRINGD
TFNSIFDIKG LTDKFPEDST KIHVATVQSL VKRTLQSDEP MPVARYDCIV VDEAHRGYIL
DKEQTEGELQ FRSQLDYVSA YRRILDHFDA VKIALTATPA LHTVQIFGEP VYRYTYRTAV
IDGFLIDQDP PIQIITRNAQ EGVYLSKGEQ VERISPQGEV INDTLEDDQD FEVADFNRGL
VIPAFNRAVC NELTNYLDPT GSQKTLVFCV TNAHADMVVE ELRAAFKKKY PQLEHDAIIK
ITGDADKDAR KVQTMITRFN KERLPNIVVT VDLLTTGVDI PSICNIVFLR KVRSRILYEQ
MKGRATRLCP EVNKTSFKIF DCVDIYSTLE SVDTMRPVVV RPKVELQTLV NEITDSETYK
ITEADGRSFA EHSHEQLVAK LQRIIGLATF NRDRSETIDK QVRRLDELCQ DAAGVNFNGF
ASRLREKGPH WSAEVFNKLP GFIARLEKLK TDINNLNDAP IFLDIDDEVV SVKSLYGDYD
TPQDFLEAFD SLVQRSPNAQ PALQAVINRP RDLTRKGLVE LQEWFDRQHF EESSLRKAWK
ETRNEDIAAR LIGHIRRAAV GDALKPFEER VDHALTRIKG ENDWSSEQLS WLDRLAQALK
EKVVLDDDVF KTGNFHRRGG KAMLQRTFDD NLDTLLGKFS DYIWDELA
Length

1,188

Mol. Wt

136.103 kDa

pI

5.9 (calculated)

Extinction coefficient

134,650 - 136,150 (calc based on 35 Y, 15 W, and 12 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:EG10459-MONOMER

UniProt (EcoliWiki Page)

UniProt:P08956

PFAM (EcoliWiki Page)

PFAM:PF04313

RefSeq (EcoliWiki Page)

RefSeq:NP_418770

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z5948-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)

hsdRMS

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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=4584818..4584858&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:b4350 (EcoliWiki Page)

NCBI GEO profiles for hsdR

microarray

GenExpDB:b4350 (EcoliWiki Page)

Summary of data for hsdR 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

GFP Fusion

Intergenic region (4584295..4584573) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:G12[8]

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Notes

Accessions Related to hsdR Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10459

EchoBASE (EcoliWiki Page)

EchoBASE:EB0454

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4350

EcoGene (EcoliWiki Page)

EcoGene:EG10459


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Notes

Links

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Evolution

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Homologs in Other Organisms

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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.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF04313


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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 1.12 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 3.6 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 7.8 7.9 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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