rnr:Gene Product(s)
{{#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 |
Rnr |
|---|---|
| Synonyms |
exoribonuclease R, RNase R[1], B4179[2][1], YjeC[2][1], Rnr[2][1], VacB[2][1] , ECK4175, JW5741, vacB, yjeC, b4179 |
| Product description |
EG11259- Exoribonuclease R; specifically required for SsrA-SmpB-dependent decay of non-stop aberrant mRNAs (Richards, 2006)[3] |
| EC number (for enzymes) | |
| edit table |
<protect></protect>
Notes
Function
<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:0005737 |
cytoplasm |
C |
Seeded from Riley et al 2006 [1]. |
Missing: evidence | ||||
| GO:0003676 |
nucleic acid binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003723 |
RNA binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003723 |
RNA binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003723 |
RNA binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003723 |
RNA binding |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0003723 |
RNA binding |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0004518 |
nuclease activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0004540 |
ribonuclease activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0004540 |
ribonuclease activity |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0009405 |
pathogenesis |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0016070 |
RNA metabolic process |
GOA:interpro |
IEA: Inferred from Electronic Annotation |
P |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0016787 |
hydrolase activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0004540 |
ribonuclease activity |
IMP: Inferred from Mutant Phenotype |
F |
Table 2: extracts of rnr mutant cells have reduced poly(A) degrading activity |
complete | |||
| GO:0016896 |
exoribonuclease activity, producing 5'-phosphomonoesters |
IDA: Inferred from Direct Assay |
F |
Fig. 3 and Table 2 |
complete | |||
| GO:0004527 |
exonuclease activity |
GOA:spkw |
IEA: Inferred from Electronic Annotation |
F |
Seeded from EcoCyc (v14.0) |
complete | ||
| GO:0008997 |
ribonuclease R activity |
IDA: Inferred from Direct Assay |
F |
Fig. 3 and Table 2 |
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 |
cca |
Experiment(s):EBI-883997 | ||
|
Protein |
infC |
Experiment(s):EBI-883997 | ||
|
Protein |
pgm |
Experiment(s):EBI-883997 | ||
|
Protein |
pssA |
Experiment(s):EBI-883997 | ||
|
Protein |
rplA |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rplB |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rplC |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rplF |
Experiment(s):EBI-883997 | ||
|
Protein |
rplI |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rplM |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rplN |
Experiment(s):EBI-883997 | ||
|
Protein |
rplO |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rpsA |
Experiment(s):EBI-883997 | ||
|
Protein |
rpsB |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rpsC |
Experiment(s):EBI-883997 | ||
|
Protein |
rpsD |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rpsE |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rpsF |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rpsG |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rpsM |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
rpsP |
Experiment(s):EBI-883997, EBI-891136 | ||
|
Protein |
intA |
Experiment(s):EBI-883997 | ||
|
Protein |
tgt |
Experiment(s):EBI-883997 | ||
|
Protein |
ycbY |
Experiment(s):EBI-883997 | ||
|
Protein |
yfiF |
Experiment(s):EBI-883997, EBI-879491 | ||
|
Protein |
ygiF |
Experiment(s):EBI-883997 | ||
|
Protein |
ihfA |
Experiment(s):EBI-891136 | ||
|
Protein |
hupA |
Experiment(s):EBI-891136 | ||
|
Protein |
rplP |
Experiment(s):EBI-891136 | ||
|
Protein |
rplT |
Experiment(s):EBI-891136 | ||
|
Protein |
rplU |
Experiment(s):EBI-891136 | ||
|
Protein |
rplV |
Experiment(s):EBI-891136 | ||
|
Protein |
rplW |
Experiment(s):EBI-891136 | ||
|
Protein |
rplX |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsH |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsI |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsK |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsN |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsO |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsR |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsT |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsU |
Experiment(s):EBI-891136 | ||
|
Protein |
rpsH |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsP |
LCMS(ID Probability):99.6 MALDI(Z-score):9.921698 | ||
|
Protein |
rplP |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsN |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsF |
LCMS(ID Probability):99.6 MALDI(Z-score):17.670398 | ||
|
Protein |
rpsT |
LCMS(ID Probability):99.6 MALDI(Z-score):2.564045 | ||
|
Protein |
hupA |
LCMS(ID Probability):99.6 | ||
|
Protein |
ihfA |
LCMS(ID Probability):99.0 | ||
|
Protein |
rpsM |
LCMS(ID Probability):99.6 MALDI(Z-score):11.502079 | ||
|
Protein |
rplU |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplW |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplI |
LCMS(ID Probability):99.6 MALDI(Z-score):30.262063 | ||
|
Protein |
rpsI |
LCMS(ID Probability):99.0 MALDI(Z-score):6.592879 | ||
|
Protein |
rpsR |
LCMS(ID Probability):99.6 | ||
|
Protein |
rpsO |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplX |
LCMS(ID Probability):99.6 MALDI(Z-score):3.597110 | ||
|
Protein |
rpsK |
LCMS(ID Probability):99.6 MALDI(Z-score):2.388265 | ||
|
Protein |
rplB |
LCMS(ID Probability):99.6 MALDI(Z-score):38.617983 | ||
|
Protein |
rplM |
LCMS(ID Probability):99.6 MALDI(Z-score):23.975877 | ||
|
Protein |
rplO |
LCMS(ID Probability):99.6 MALDI(Z-score):21.852990 | ||
|
Protein |
rpsU |
LCMS(ID Probability):99.6 MALDI(Z-score):3.411533 | ||
|
Protein |
rpsD |
LCMS(ID Probability):99.6 MALDI(Z-score):35.575045 | ||
|
Protein |
rpsC |
MALDI(Z-score):32.945078 | ||
|
Protein |
rplT |
LCMS(ID Probability):99.6 | ||
|
Protein |
rplA |
LCMS(ID Probability):99.6 MALDI(Z-score):50.772162 | ||
|
Protein |
infC |
MALDI(Z-score):20.289543 | ||
|
Protein |
rplF |
LCMS(ID Probability):97.9 MALDI(Z-score):11.134401 | ||
|
Protein |
rplD |
LCMS(ID Probability):99.6 MALDI(Z-score):29.084634 | ||
|
Protein |
pssA |
MALDI(Z-score):19.741475 | ||
|
Protein |
yibL |
LCMS(ID Probability):98.5 | ||
|
Protein |
yfiF |
MALDI(Z-score):26.783167 | ||
| 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
<protect>
Physical Properties
See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.
| Name | |
|---|---|
| Sequence |
MTKIFIRDDN GGTEMSQDPF QEREAEKYAN PIPSREFILE HLTKREKPAS RDELAVELHI EGEEQLEGLR RRLRAMERDG QLVFTRRQCY ALPERLDLVK GTVIGHRDGY GFLRVEGRKD DLYLSSEQMK TCIHGDQVLA QPLGADRKGR REARIVRVLV PKTSQIVGRY FTEAGVGFVV PDDSRLSFDI LIPPDQIMGA RMGFVVVVEL TQRPTRRTKA VGKIVEVLGD NMGTGMAVDI ALRTHEIPYI WPQAVEQQVA GLKEEVPEEA KAGRVDLRDL PLVTIDGEDA RDFDDAVYCE KKRGGGWRLW VAIADVSYYV RPSTPLDREA RNRGTSVYFP SQVIPMLPEV LSNGLCSLNP QVDRLCMVCE MTVSSKGRLT GYKFYEAVMS SHARLTYTKV WHILQGDQDL REQYAPLVKH LEELHNLYKV LDKAREERGG ISFESEEAKF IFNAERRIER IEQTQRNDAH KLIEECMILA NISAARFVEK AKEPALFRIH DKPSTEAITS FRSVLAELGL ELPGGNKPEP RDYAELLESV ADRPDAEMLQ TMLLRSMKQA IYDPENRGHF GLALQSYAHF TSPIRRYPDL TLHRAIKYLL AKEQGHQGNT TETGGYHYSM EEMLQLGQHC SMAERRADEA TRDVADWLKC DFMLDQVGNV FKGVISSVTG FGFFVRLDDL FIDGLVHVSS LDNDYYRFDQ VGQRLMGESS GQTYRLGDRV EVRVEAVNMD ERKIDFSLIS SERAPRNVGK TAREKAKKGD AGKKGGKRRQ VGKKVNFEPD SAFRGEKKTK PKAAKKDARK AKKPSAKTQK IAAATKAKRA AKKKVAE |
| Length |
827 |
| Mol. Wt |
93.689 kDa |
| pI |
8.8 (calculated) |
| Extinction coefficient |
64,750 - 65,875 (calc based on 25 Y, 5 W, and 9 C residues) |
| edit table |
Domains/Motifs/Modification Sites
|
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.
|
<motif_map/> |
|
Structure
| </protect>
Structure figures<protect> | ||||||
Notes
Gene Product Resources
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
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
|
Escherichia coli str. K-12 substr. MG1655 | ||
| edit table |
<protect></protect>
Notes
Links
| Name | URL | Comments |
|---|---|---|
| edit table |
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
- ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
- ↑ Riley, M et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot--2005. Nucleic Acids Res. 34 1-9 PubMed
- ↑ Cheng, ZF et al. (1998) The vacB gene required for virulence in Shigella flexneri and Escherichia coli encodes the exoribonuclease RNase R. J. Biol. Chem. 273 14077-80 PubMed
- ↑ 6.0 6.1 Cheng, ZF & Deutscher, MP (2002) Purification and characterization of the Escherichia coli exoribonuclease RNase R. Comparison with RNase II. J. Biol. Chem. 277 21624-9 PubMed
- ↑ 7.00 7.01 7.02 7.03 7.04 7.05 7.06 7.07 7.08 7.09 7.10 7.11 7.12 7.13 7.14 7.15 7.16 7.17 7.18 7.19 7.20 7.21 7.22 7.23 7.24 7.25 7.26 7.27 7.28 7.29 7.30 7.31 7.32 7.33 7.34 7.35 7.36 7.37 7.38 7.39 7.40 7.41 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
- ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 8.29 8.30 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
- ↑ 9.0 9.1 9.2 9.3 9.4 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
Categories
- GO:0005737 ! cytoplasm
- GO:0003676 ! nucleic acid binding
- GO:0003723 ! RNA binding
- GO:0004518 ! nuclease activity
- GO:0004540 ! ribonuclease activity
- GO:0009405 ! pathogenesis
- GO:0016070 ! RNA metabolic process
- GO:0016787 ! hydrolase activity
- GO:0016896 ! exoribonuclease activity, producing 5'-phosphomonoesters
- GO:0004527 ! exonuclease activity
- GO:0008997 ! ribonuclease R activity
- Proteins
