hsdR:Gene Product(s): Difference between revisions

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!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
Protein
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[[hsdM:Gene_Product(s)|hsdM]]
hsdM
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Protein
Protein
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[[rplL:Gene_Product(s)|rplL]]
rplL
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!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
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View models at:
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P08956 Protein Model Portal]
* [http://www.proteinmodelportal.org/query/uniprot/P08956 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P08956 PSI-PRED (P08956)]
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P08956 Genomes TO Protein (P08956)] (GTOP)


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!|Database!!Accession!!Notes
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[ASAP]]
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ASAP:ABE-0014264
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P08956 UniProtKB/Swiss-Prot:P08956]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:EG10459
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG10459
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/gene?term=948878 GeneID:948878]
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Escherichia coli str. K-12 substr. MG1655
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[[RegulonDB]]
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RegulonDB:ECK120000452
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB0454
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 21:15, 17 February 2015

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

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

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)
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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.

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

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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[5]

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

Protein

hsdM

PMID:15690043[5]

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

Protein

lpdA

PMID:15690043[5]

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

Protein

rplL

PMID:15690043[5]

Experiment(s):EBI-894477

Protein

hsdM

PMID:19402753[6]

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

Protein

rplL

PMID:19402753[6]

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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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)

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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 Notes References

Domain

771..849

PF00271 Helicase conserved C-terminal domain

PMID:19920124[7]

Domain

257..414

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

PMID:19920124[7]

Domain

460..641

PF04851 Type III restriction enzyme, res subunit

PMID:19920124[7]

Domain

858..1185

PF12082 Domain of unknown function (DUF3559)

PMID:19920124[7]

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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=hsdR taxon=562,83333 </beststructure>

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 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: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

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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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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 5.3 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  6. ↑ 6.0 6.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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