Difference between revisions of "Sandbox"

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−
{{PubMed|19383706}}
+
* '''Description:''' Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon <br/><br/>
−
 
 
−
* '''Description:''' similar to ABC transporter (membrane protein) <br/><br/>
 
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''yhcI''
+
|''ccpA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''graR, alsA, amyR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
+
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates carbon catabolite repression (CCR)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 34 kDa, 6.336 
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/nucleosides_catabolism.html Nucleoside catabolism], [http://subtiwiki.uni-goettingen.de/pathways/gene_regulation_nucleotides.html Nucleotides (regulation)], [http://subtiwiki.uni-goettingen.de/pathways/ile_val_leu.html Ile, Leu, Val],<br/>[http://subtiwiki.uni-goettingen.de/pathways/histidine.html His], [http://subtiwiki.uni-goettingen.de/pathways/CoA_synthesis.html Coenzyme A], [http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 939 bp, 313 aa
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 36,8 kDa, 5.06
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhcH]]'', ''[[cspB]]''
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 amino acids
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12737&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[aroA]]'', ''[[motP]]''
−
 
+
|-
−
<pubmed>19383706 </pubmed>
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14952&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yhcI_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ccpA_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
Line 33: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/><br/><br/>
 +
 
  
 
=The gene=
 
=The gene=
Line 39: Line 38:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU09090
+
* '''Locus tag:''' BSU29740
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
Loss of carbon catabolite repression.
 +
Loss of PTS-dependent sugar transport due to excessive phosphorylation of [[PtsH |HPr]] by [[HprK]].
 +
The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yhbIJ-yhcABCDEFGHI.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpA-motPS.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11587]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10376]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 56: Line 58:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' transcriptional regulator of carbon catabolite repression (CCR)
  
−
* '''Protein family:'''
+
* '''Protein family:''' LacI family
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes controlled by CcpA ===
 +
 +
* '''Activation by CcpA:''' ''[[pta]]'', ''[[ackA]]'', ''[[ilvB]]-[[ilvH]]-[[ilvC]]-[[leuA]]-[[leuB]]-[[leuC]]-[[leuD]]''
 +
 +
* '''Repression by CcpA:''' ''[[abbA]], [[amyE]]'', ''[[bglP]]-[[bglH]]'', ''[[bglS]]'', ''[[cccA]]'', ''[[citZ]]-[[icd]]-[[mdh]]'', ''[[levD]]-[[levE]]-[[levF]]-[[levG]]-[[sacC]]'', ''[[licB]]-[[licC]]-[[licA]]-[[licH]]'', ''[[phoP]]-[[phoR]]'', ''[[xylA]]-[[xylB]]'', ''[[xynP]]-[[xynB]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 67: Line 75:
  
 
* '''Domains:'''  
 
* '''Domains:'''  
 +
** HTH lacI-type Domain (1 – 58)
 +
** DNA binding Domain  (6 – 25)
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' [[PtsH |HPr]]-Ser46-P, Crh-Ser-46-P
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:'''glucose-6-phosphate, fructose-1,6-bisphosphate [http://www.ncbi.nlm.nih.gov/pubmed/17376479?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum Pubmed]
  
−
* '''Interactions:'''
+
* '''Interactions:''' CcpA-[[PtsH |HPr]] [http://www.ncbi.nlm.nih.gov/pubmed/15369672?ordinalpos=3&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed], CcpA-[[Crh]] [http://www.ncbi.nlm.nih.gov/pubmed/16316990?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum PubMed]
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' CcpA-Crh-DNA-complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326 NCBI], complex with P-Ser-[[PtsH |HPr]] and sulphate ions [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39857 NCBI]
−
 
 
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54593 P54593]
 
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU09090]
+
\* UniProt entry: [http://www.uniprot.org/uniprot/P25144 P25144]
  
−
* '''E.C. number:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[ccpA]] [[motP]] [[motS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' constitutively  expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
  
−
* '''Regulatory mechanism:'''
+
* '''Additional information:''' there are about 3.000 molecules of CcpA per cell [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 PubMed]
−
 
 
−
* '''Additional information:'''  
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ''[[ccpA]]''), available in [[Stülke]] lab
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pGP643 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''Antibody:''' available in [[Hillen]] and [[Stülke]] labs
  
−
* '''Antibody:'''
+
=Labs working on this gene/protein=
  
−
=Labs working on this gene/protein=
+
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
 +
 
 +
[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]
 +
 
 +
[[Milton H. Saier]], University of California at San Diego, USA [http://biology.ucsd.edu/faculty/saier.html Homepage]
 +
 
 +
[[Yasutaro Fujita]], University of Fukuyama, Japan
 +
 
 +
[[Stülke|Jörg Stülke]], University of Göttingen, Germany [http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 +
 
 +
[[Oscar Kuipers]], University of Groningen, The Netherlands
 +
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 139:
 
=References=
 
=References=
  
−
<pubmed>10092453,, </pubmed>
+
'''Reviews'''
 +
 
 +
<pubmed> 8598282 , 19202299,14665673,18628769 ,18359269, 18628769    </pubmed>
 +
 
 +
'''General and physiological studies'''
 +
 
 +
<pubmed>1904524 ,10941796 ,12123463,8000527, 18757537,16547058,14523131 </pubmed>
 +
 
 +
'''Global analyses (proteome, transcriptome)'''
 +
 
 +
<pubmed>12850135 ,11251851,10559165, 11160890,17183215 </pubmed>
 +
 
 +
'''Repression of target genes by CcpA'''
 +
 
 +
<pubmed>15150224 ,16166551 ,11929549 , 7913927 ,17827291 ,11985717 ,12100558,7592486  </pubmed>
 +
 
 +
'''Positive regulation of gene expression by CcpA'''
 +
 
 +
<pubmed>8226682 ,12193635 ,10559153 ,15916605, 9811655 ,10986270 </pubmed>
 +
 
 +
'''Control of CcpA activity'''
 +
 
 +
<pubmed>7623661 ,9973552 ,9334231 ,12051938, 9689125 </pubmed>
 +
 
 +
'''CcpA-DNA interaction'''
 +
 
 +
<pubmed>8596444 ,10666464 ,15885105,7665492 ,9254709  </pubmed>
 +
 
 +
'''Functional analysis of CcpA'''
 +
 
 +
<pubmed>10383986 ,10601226 ,11557150,9252590 ,9988473  </pubmed>
 +
 
 +
'''Structural analyses'''
 +
 
 +
<pubmed>15369672 ,16316990 ,17376479 </pubmed>

Revision as of 15:37, 15 July 2009

  • Description: Carbon catabolite control protein A, involved in glucose regulation of many genes; represses catabolic genes and activates genes involved in excretion of excess carbon

Gene name ccpA
Synonyms graR, alsA, amyR
Essential no
Product transcriptional regulator
Function mediates carbon catabolite repression (CCR)
Metabolic function and regulation of this protein in SubtiPathways:
Nucleoside catabolism, Nucleotides (regulation), Ile, Leu, Val,
His, Coenzyme A, Central C-metabolism
MW, pI 36,8 kDa, 5.06
Gene length, protein length 1002 bp, 334 amino acids
Immediate neighbours aroA, motP
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CcpA context.gif
This image was kindly provided by SubtiList








The gene

Basic information

  • Locus tag: BSU29740

Phenotypes of a mutant

Loss of carbon catabolite repression. Loss of PTS-dependent sugar transport due to excessive phosphorylation of HPr by HprK. The mutant is unable to grow on a minimal medium with glucose and ammonium as the only sources of carbon and nitrogen, respectively.

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcriptional regulator of carbon catabolite repression (CCR)
  • Protein family: LacI family
  • Paralogous protein(s):

Genes controlled by CcpA

Extended information on the protein

  • Kinetic information:
  • Domains:
    • HTH lacI-type Domain (1 – 58)
    • DNA binding Domain (6 – 25)
  • Modification:
  • Cofactor(s): HPr-Ser46-P, Crh-Ser-46-P
  • Effectors of protein activity:glucose-6-phosphate, fructose-1,6-bisphosphate Pubmed
  • Localization:

Database entries

  • Structure: CcpA-Crh-DNA-complex NCBI, complex with P-Ser-HPr and sulphate ions NCBI

\* UniProt entry: P25144

  • KEGG entry: [3]

Additional information

Expression and regulation

  • Sigma factor:
  • Regulation: constitutively expressed PubMed
  • Additional information: there are about 3.000 molecules of CcpA per cell PubMed

Biological materials

  • Mutant: QB5407 (spc), GP302 (erm), GP300 (an in frame deletion of ccpA), available in Stülke lab
  • Expression vector: pGP643 (N-terminal Strep-tag, purification from B. subtilis, for SPINE, in pGP380), available in Stülke lab
  • lacZ fusion:
  • GFP fusion:

Labs working on this gene/protein

Wolfgang Hillen, Erlangen University, Germany Homepage

Richard Brennan, Houston, Texas, USA Homepage

Milton H. Saier, University of California at San Diego, USA Homepage

Yasutaro Fujita, University of Fukuyama, Japan

Jörg Stülke, University of Göttingen, Germany Homepage

Oscar Kuipers, University of Groningen, The Netherlands Homepage

Your additional remarks

References

Reviews


General and physiological studies


Global analyses (proteome, transcriptome)


Repression of target genes by CcpA


Positive regulation of gene expression by CcpA


Control of CcpA activity


CcpA-DNA interaction


Functional analysis of CcpA


Structural analyses

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