hsdR:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

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[1], B4350[2][1], Hsr[2][1], Hsp[2][1], HsdR[2][1] , ECK4340, hsp, hsr, JW4313, b4350

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): hsdRMS[3]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


HsdR acts as a chaperone in hsdS mutant to allow DNA binding.[4]



Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


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]

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

98.74 minutes 

MG1655: 4584838..4581272
<gbrowseImage> name=NC_000913:4581272..4584838 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4564736..4561224
<gbrowseImage> name=NC_012967:4561224..4564736 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4519756..4523322
<gbrowseImage> name=NC_012759:4519756..4523322 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4591495..4587929
<gbrowseImage> name=NC_007779:4587929..4591495 source=W3110 preset=GeneLocation </gbrowseImage>

edit table

</protect>

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes
edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

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


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]


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

Resource Resource Type Source Notes/Reference

JW4313

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTATGGGCgTTAAATATTTGGACAGGCCCG

Primer 2:CCGGCCAGCTCGTCCCAGATATA

12G5

Kohara Phage

Genobase

PMID:3038334

10H12

Kohara Phage

Genobase

PMID:3038334

7C1

Kohara Phage

Genobase

PMID:3038334

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

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10459

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10459

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000452

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948878

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0454

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014264

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name

HsdR

Synonyms

endonuclease R[1], B4350[2][1], Hsr[2][1], Hsp[2][1], HsdR[2][1] , ECK4340, hsp, hsr, JW4313, b4350

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)
edit table

<protect></protect>

Notes

Function

[back to top]


<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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006935

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007409

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:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0347

F

Seeded from EcoCyc (v14.0)

complete

GO:0004519

endonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007409

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006935

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0006304

DNA modification

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007409

P

Seeded from EcoCyc (v14.0)

complete

GO:0009035

Type I site-specific deoxyribonuclease activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.21.3

F

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

GO:0016787

hydrolase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006935

F

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

edit table

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-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

Protein

hsdM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):28.932061

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

edit table

</protect>

Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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 

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)

edit table


Domains/Motifs/Modification Sites

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

Type Residues Description Notes References

Domain

771..849

PF00271 Helicase conserved C-terminal domain

PMID:19920124

Domain

257..414

PF04313 Type I restriction enzyme R protein N terminus (HSDR_N)

PMID:19920124

Domain

460..641

PF04851 Type III restriction enzyme, res subunit

PMID:19920124

Domain

858..1185

PF12082 Domain of unknown function (DUF3559)

PMID:19920124

edit table

<motif_map/>

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

Structures

<beststructure> gene=hsdR taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:226524764

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948878

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014264

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P08956

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10459

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10459

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948878

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000452

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0454

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

1.14E+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

404

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

186

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

338

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

hsdRMS

edit table
Figure courtesy of RegulonDB

</protect>

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

[back to top]


<protect><gbrowseImage> name=NC_000913:4584818..4584858 source=MG1655 flip=1 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

</protect>

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

[back to top]


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

Allele Name Mutation Phenotype Reference
edit table


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

Type Reference Notes

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

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

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

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ04; Well:G12[7]

edit table

<protect></protect>

Notes

Accessions Related to hsdR Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10459

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0454

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4350

EcoGene

EcoGene:EG10459

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000452

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014264

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments
edit table

</protect>


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00271 Helicase conserved C-terminal domain

Pfam (EcoliWiki Page)

PF04313 Type I restriction enzyme R protein N terminus (HSDR_N)

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Pfam (EcoliWiki Page)

PF04851 Type III restriction enzyme, res subunit

Pfam (EcoliWiki Page)

PF12082 Domain of unknown function (DUF3559)

EcoCyc

EcoCyc:EG10459

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10459

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000452

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0454

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0014264

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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 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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=hsdR:On_One_Page&oldid=222737"