|
|
| (69 intermediate revisions by 6 users not shown) |
| Line 1: |
Line 1: |
| * '''Description:''' [[RNase]] Y, 5' end sensitive endoribonuclease, involved in the degradation/processing of mRNA<br/><br/>
| | {{#bank: Rny}} |
|
| |
|
| {| align="right" border="1" cellpadding="2"
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"|'''Gene name'''
| |
| |''rny''
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ymdA''
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''Essential''' || yes
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''Product''' || [[RNase]] Y
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"|'''Function''' || Initiates [[S-box]] [[riboswitch]] RNA turnover, required for the processing <br/>of the ''[[gapA]]'' operon mRNA, depletion of RNase Y increases bulk <br/>mRNA stability.
| |
| |-
| |
| |colspan="2" style="background:#FAF8CC;" align="center"| '''Regulatory function of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 58,7 kDa, 5.39
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1560 bp, 520 amino acids
| |
| |-
| |
| |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[pbpX]]'', ''[[ymdB]]''
| |
| |-
| |
| |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13569]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
| |
| |-
| |
| |-
| |
| |-
| |
| |colspan="2" | '''Genetic context''' <br/> [[Image:rny_context.gif]]
| |
| <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
| |
| |-
| |
| |}
| |
|
| |
| __TOC__
| |
|
| |
| <br/><br/><br/><br/><br/><br/>
| |
|
| |
| =The gene=
| |
|
| |
| === Basic information ===
| |
|
| |
| * '''Locus tag:''' BSU16960
| |
|
| |
| ===Phenotypes of a mutant ===
| |
|
| |
| essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
| |
|
| |
| === Database entries ===
| |
|
| |
| * '''DBTBS entry:''' no entry
| |
|
| |
| * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13420]
| |
|
| |
| === Additional information===
| |
|
| |
| =The protein=
| |
|
| |
| === Basic information/ Evolution ===
| |
|
| |
| * '''Catalyzed reaction/ biological activity:''' [[RNase]] Y cleaves [[S-box]] [[riboswitch]] RNAs ''in vivo'' and ''in vitro''; preference for 5' monophosphorylated substrate ''in vitro'', endonucleolytic cleavage; required for the processing of the ''[[gapA]]'' operon mRNA [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed], cleavage activity appears sensitive to downstream secondary structure.
| |
|
| |
| * '''Protein family:''' Member of the HD superfamily of metal-dependent phosphohydrolases; 2',3' cyclic nucleotide phosphodiesterase family (according to Swiss-Prot)
| |
|
| |
| * '''Paralogous protein(s):'''
| |
|
| |
| === Extended information on the protein ===
| |
|
| |
| * '''Kinetic information:'''
| |
|
| |
| * '''Domains:'''
| |
| ** transmembrane domain (4–24)
| |
| ** KH domain (210–273)
| |
| ** HD domain (336–429)
| |
|
| |
| * '''Modification:'''
| |
|
| |
| * '''Cofactor(s):''' requires Mg+2, which can be replaced by Zn+2 or Mn+2 ions
| |
|
| |
| * '''Effectors of protein activity:''' appears sensitive to downstream secondary structure
| |
|
| |
| * '''Interactions:''' [[Rny]]-[[PfkA]], [[Rny]]-[[Eno]], [[Rny]]-[[PnpA]], [[Rny]]-[[RnjA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
| |
|
| |
| * '''Localization:''' cell membrane, single-pass membrane protein {{PubMed|18763711,17005971,19820159}}
| |
|
| |
| === Database entries ===
| |
|
| |
| * '''Structure:'''
| |
|
| |
| * '''UniProt:''' [http://www.uniprot.org/uniprot/O31774 O31774]
| |
|
| |
| * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16960]
| |
|
| |
| * '''E.C. number:''' [http://www.expasy.org/enzyme/3.1.4.16 3.1.4.16]
| |
|
| |
| === Additional information===
| |
|
| |
| required for the processing of the ''[[gapA]]'' operon mRNA
| |
| =Expression and regulation=
| |
|
| |
| * '''Operon:''' ''[[rny]]-[[ymdB]]''
| |
|
| |
| * '''Sigma factor:'''
| |
|
| |
| * '''Regulation:''' constitutive
| |
|
| |
| * '''Regulatory mechanism:'''
| |
|
| |
| * '''Additional information:''' there is a terminator between ''rny'' and ''[[ymdB]]'', most transcripts terminate there
| |
|
| |
| =Biological materials =
| |
|
| |
| * '''Mutant:''' essential!!!!, 4043 (''rny'' under p-spac control, ''cat''), GP193 (''rny'' under p-xyl control, ''cat''), both available in [[Stülke]] lab; SSB447 (rny under P-spac control, "erm") available in [[Putzer]] lab.
| |
|
| |
| * '''Expression vector:'''
| |
| ** N-terminal Strep-tag, expression in ''E. coli'', in [[pGP172]]: pGP441, available in [[Stülke]] lab
| |
| ** N-terminal Strep-tag, for [[SPINE]], expression in ''B. subtilis'', in [[pGP380]]: pGP775 , available in [[Stülke]] lab
| |
| **Expression of RNase Y missing the N-terminal transmembrane domain (25aa) as an intein fusion in E. coli (no tag left in the purified protein) available in the [[Putzer]] lab
| |
| ** wild type ''rny'', expression in ''B. subtilis'', in [[pBQ200]]: pGP1201, available in [[Stülke]] lab
| |
| ** there is also a series of domain constructs present in [[pBQ200]], all available in [[Stülke]] lab
| |
|
| |
| * '''lacZ fusion:''' pGP459 (in [[pAC7]]), available in [[Stülke]] lab
| |
|
| |
| * '''GFP fusion:''' B. subtilis 3569 (amyE:: (p-xyl rny-gfpmut1-spc)), available in [[Errington]] lab
| |
|
| |
| * '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
| |
|
| |
| * '''Antibody:''' available in [[van Dijl]] and [[Stülke]] labs
| |
|
| |
| =Labs working on this gene/protein=
| |
|
| |
| [[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]
| |
|
| |
| [[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
| |
|
| |
| =Your additional remarks=
| |
|
| |
| =References=
| |
|
| |
|
| |
| <pubmed>18763711,19193632,17005971 19779461 19820159 </pubmed>
| |
|
| |
| [[Category:Protein-coding genes]]
| |
