Difference between revisions of "Sandbox"

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(Replaced content with '=== Database entries === * '''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 |H…')
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* '''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/>
 
 
{| align="right" border="1" cellpadding="2"
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|''ccpA''
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''graR, alsA, amyR''
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Function''' || mediates carbon catabolite repression (CCR)
 
|-
 
|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"| '''MW, pI''' || 36,8 kDa, 5.06
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1002 bp, 334 amino acids
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[aroA]]'', ''[[motP]]''
 
|-
 
|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:ccpA_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:''' BSU29740
 
 
===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 ===
 
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpA-motPS.html]
 
 
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10376]
 
 
=== 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 ===
 
 
* '''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 ===
 
 
* '''Kinetic information:'''
 
 
* '''Domains:'''
 
** HTH lacI-type Domain (1 – 58)
 
** DNA binding Domain  (6 – 25)
 
 
* '''Modification:'''
 
 
* '''Cofactor(s):''' [[PtsH |HPr]]-Ser46-P, Crh-Ser-46-P
 
 
* '''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:''' 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:'''
 
 
 
=== Database entries ===
 
=== Database entries ===
  
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]
 
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU29740]
 
=== Additional information===
 
 
=Expression and regulation=
 
 
* '''Operon:''' ''[[ccpA]] [[motP]] [[motS]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/16547058 PubMed]
 
 
* '''Sigma factor:'''
 
 
* '''Regulation:''' constitutively  expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/18757537 PubMed]
 
 
* '''Additional information:''' there are about 3.000 molecules of CcpA per cell [http://www.ncbi.nlm.nih.gov/sites/entrez/8000527 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:'''
 
 
* '''Antibody:''' available in [[Hillen]] and [[Stülke]] labs
 
 
=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=
 
 
=References=
 
 
'''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>
 
 
[[Category:Protein-coding genes]]
 

Revision as of 09:10, 21 July 2009

Database entries

  • Structure: CcpA-Crh-DNA-complex NCBI, complex with P-Ser-HPr and sulphate ions NCBI
  • KEGG entry: [1]