Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' enolase, glycolytic/ gluconeogenic enzyme, [[universally conserved protein]]<br/><br/>
+
* '''Description:''' replication initiation 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'''
−
|''eno''
+
|''dnaA''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''dnaH, dnaJ, dnaK ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || enolase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || replication initiation protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || enzyme in glycolysis/ gluconeogenesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || [[DNA replication]]
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/Eno Eno]
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/DnaA DnaA]
 
|-
 
|-
−
|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/carbon_flow.html Central C-metabolism]'''
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 50 kDa, 6.035 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46,4 kDa, 4.49
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1338 bp, 446 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1290 bp, 430 amino acids
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpmH]]'', ''[[dnaN]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvbK]]'', ''[[pgm]]''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11777&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15395&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:DnaA_dnaN_yaaA_recF_yaaB_gyrB_context.png]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:eno_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>
 
|-
 
|-
−
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=eno_3476555_3477847_-1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:eno_expression.png|500px]]
+
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaA_410_1750_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:dnaA_expression.png|500px]]
 
|-
 
|-
 
|}
 
|}
Line 39: Line 37:
 
<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
 
<br/><br/><br/><br/>
 +
 +
 +
<br/><br/>
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[carbon core metabolism]]}},
+
{{SubtiWiki category|[[DNA replication]]}},
−
{{SubtiWiki category|[[membrane proteins]]}},
+
{{SubtiWiki category|[[essential genes]]}}
−
{{SubtiWiki category|[[phosphoproteins]]}},
 
−
{{SubtiWiki category|[[universally conserved proteins]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
−
{{SubtiWiki regulon|[[CggR regulon]]}}
+
{{SubtiWiki regulon|[[Spo0A regulon]]}}
−
 
+
=The [[DnaA regulon]]=
 
=The gene=
 
=The gene=
  
 
=== Basic information ===
 
=== Basic information ===
−
* '''Locus tag:''' BSU33900
+
 
 +
* '''Locus tag:''' BSU00010
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
* no growth on LB, requires glucose and malate
+
 
−
* essential according to Kobayashi et al. on LB  [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cggR-gapA-pgk-tpiA-pgm-eno.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dnaAN.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10899]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10065]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 70: Line 71:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2-phospho-D-glycerate = phosphoenolpyruvate + H<sub>2</sub>O (according to Swiss-Prot) 2-phospho-D-glycerate = phosphoenolpyruvate + H(2)O
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' enolase family (according to Swiss-Prot)
+
* '''Protein family:''' dnaA family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 78: Line 79:
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
  
−
* '''Kinetic information:''' reversible Michaelis-Menten [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
+
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''Domains:''' AAA+ domain
−
** substrate binding domain (366–369)
 
  
−
* '''Modification:''' phosphorylation on Thr-141 AND Ser-259 AND Tyr-281 AND Ser-325 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/16493705 PubMed], [http://www.ncbi.nlm.nih.gov/pubmed/17726680 PubMed]
+
* '''Modification:'''
  
−
* '''Cofactor(s):''' Mg2+
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
−
** Inhibited by EDTA [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
+
** [[SirA]] displaces [[DnaA]] from the replication origin {{PubMed|19682252}}
 +
** [[YabA]] inhibits co-operative binding of DnaA to the ''oriC'' DNA {{PubMed|21895792}}
 +
** DnaA helix formation (and thus replication initiation) is inhibited by the interaction of [[Soj]] with the AAA+ domain of DnaA {{PubMed|22286949}}
  
 
* '''[[SubtInteract|Interactions]]:'''
 
* '''[[SubtInteract|Interactions]]:'''
−
** forms octamers {{PubMed|22198292}}
+
** [[DnaA]] assembles into a right-handed helical oligomer built upon interactions between neighbouring AAA+ domains
−
** part of the [[RNA degradosome]]  {{PubMed|19193632}}
+
** [[Soj]]-[[DnaA]] {{PubMed|22286949}}  
−
** [[Eno]]-[[PfkA]] {{PubMed|19193632}}, K(D) of the interaction: 40 nM {{PubMed|22198292}}
+
** [[DnaA]]-[[YabA]], [[DnaA]]-[[YabA]]-[[DnaN]] {{PubMed|12060778}}  
−
** [[Eno]]-[[Rny]] {{PubMed|19193632,21803996}}, K(D) of the interaction: 100 nM {{PubMed|22198292}}
+
** [[DnaA]]-[[DnaD]] [http://www.ncbi.nlm.nih.gov/sites/entrez/11222620 PubMed]
−
** [[Eno]]-[[CshA]] {{PubMed|20572937}}
+
** [[SirA]]-[[DnaA]] {{PubMed|19682252,21239581}}
 +
** [[YqaH]]-[[DnaA]] {{PubMed|12060778}}  
  
−
* '''[[Localization]]:'''
+
* '''[[Localization]]:''' throughout the cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/10844689 PubMed]
−
** cytoplasm [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
−
** membrane associated [http://www.ncbi.nlm.nih.gov/sites/entrez/18763711 PubMed]
 
−
** exported, this requires a long, unbent α-helix (from A108 to L126)  {{PubMed|15003462,21856851}}
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''  
+
* '''Structure:'''
−
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=4A3R 4A3R] {{PubMed|22198292}}
 
−
** [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1W6T 1W6T] (from ''Streptococcus pneumoniae'') {{PubMed|15476816}}
 
  
−
* '''UniProt:''' [http://www.uniprot.org/uniprot/P37869 P37869]
+
* '''UniProt:''' [http://www.uniprot.org/uniprot/P05648 P05648]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU33900]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00010]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.11 4.2.1.11]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
* Enolase is a [[moonlighting proteins|moonlighting protein]]. [http://www.ncbi.nlm.nih.gov/sites/entrez/19193632 PubMed]
 
−
* There are indications that this enzyme is an octamer [http://www.ncbi.nlm.nih.gov/sites/entrez/25885 PubMed]
 
−
* [[universally conserved protein]]
 
−
* extensive information on the structure and enzymatic properties of Eno can be found at [http://www.proteopedia.org/wiki/index.php/Enolase Proteopedia]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[dnaA]]-[[dnaN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
−
** ''[[cggR]]-[[gapA]]-[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
 
−
** ''[[pgk]]-[[tpiA]]-[[pgm]]-[[eno]]'' {{PubMed|11489127}}
 
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=eno_3476555_3477847_-1 eno] {{PubMed|22383849}}
+
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=dnaA_410_1750_1 dnaA] {{PubMed|22383849}}
  
−
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=eno_3476555_3477847_-1 eno] {{PubMed|22383849}}
+
* '''Sigma factor:''' [[SigA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
  
−
* '''Sigma factor:''' [[SigA]] {{PubMed|11489127}}
+
* '''Regulation:''' negatively controlled by [[DnaA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2168872 PubMed] and [[Spo0A]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
 +
** repressed under conditions that trigger sporulation ([[Spo0A]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulatory mechanism:'''  
−
** expression activated by glucose (3.3 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
+
** [[Spo0A]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/14651647 PubMed]
−
** ''[[cggR]]'': induced by glycolytic substrates [[CggR]] {{PubMed|11489127}}
 
−
** ''[[pgk]]'': constitutive {{PubMed|11489127}}
 
−
 
 
−
* '''Regulatory mechanism:''' transcription repression by [[CggR]] {{PubMed|11489127}}
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 143: Line 132:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''  
+
* '''Mutant:'''
−
** GP594 (''eno''::''cat''), available in [[Stülke]] lab
 
−
** GP599 (''eno''::''erm''), available in [[Stülke]] lab
 
−
** GP698 (''eno''-''[[pgm]]''::''cat''), available in [[Stülke]] lab
 
−
 
 
−
* '''Expression vector:'''
 
−
** pGP1426 (expression of ''[[eno]]'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
 
−
** pGP1500 (expression of ''[[pgm]]'' and ''[[eno]]'' in ''B. subtilis'', in [[pBQ200]]), available in [[Stülke]] lab
 
−
** pGP563 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab
 
−
** pGP1276 (N-terminal Strep-tag, purification from ''E. coli'', in [[pGP172]]), available in [[Stülke]] lab
 
−
** pGP93 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), available in [[Stülke]] lab
 
−
** GP1215 (''eno''-''Strep'' ''(spc)''), purification from ''B. subtilis'', for [[SPINE]], available in [[Stülke]] lab
 
  
 +
* '''Expression vector:'''
 +
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
−
** see ''[[pgk]]''
 
  
−
* '''GFP fusion:''' pHT315-yfp-eno, available in [[Mijakovic]] lab
+
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
−
* '''FLAG-tag construct:''' GP1214 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
+
* '''Antibody:'''
  
−
* '''Antibody:''' available in [[Stülke]] lab
+
=Labs working on this gene/protein=
 +
[[Philippe Noirot]], Jouy-en-Josas, France [http://locus.jouy.inra.fr/cms/index.php?id=18 homepage]
  
−
=Labs working on this gene/protein=
+
[[Peter Graumann]], Freiburg University, Germany [http://www.biologie.uni-freiburg.de/data/bio2/graumann/index.htm homepage]
  
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
+
[[Alan Grossman]], MIT, Cambridge, MA, USA
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 176: Line 155:
 
=References=
 
=References=
 
==Reviews==
 
==Reviews==
−
<pubmed> 8994873 </pubmed>
+
<pubmed> 20157337 21035377 21639790</pubmed>
−
==Subcellular localization of enolase==
+
==The [[DnaA regulon]]==
−
'''Additional publications:''' {{PubMed|21856851}}
+
<pubmed> 16120674, </pubmed>
−
<pubmed> 16479537 18763711 15003462 20497499 </pubmed>
+
==Original publications==
−
 
+
'''Additional publications:''' {{PubMed|22396664,21911367}}  
−
==Other original publications==
+
<pubmed>18854156,19011033, 11222620,14651647,17140409 10844689 ,11222620 12060778 16461910 2987848 2168872 11207367, 19737352 19081080 17932079 19968790 19682252 20511500 21097613 21239581 21895792 22286949</pubmed>
−
<pubmed> 17726680, 17218307, 12850135, 19193632, 11489127, 8021172, 17505547, 25885, 20572937 15476816 9988532 ,21803996 22198292 </pubmed>
 
  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 11:45, 18 April 2012

  • Description: replication initiation protein

Gene name dnaA
Synonyms dnaH, dnaJ, dnaK
Essential yes PubMed
Product replication initiation protein
Function DNA replication
Interactions involving this protein in SubtInteract: DnaA
MW, pI 50 kDa, 6.035
Gene length, protein length 1338 bp, 446 aa
Immediate neighbours rpmH, dnaN
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
DnaA dnaN yaaA recF yaaB gyrB context.png
This image was kindly provided by SubtiList
Expression at a glance   PubMed
DnaA expression.png
























Categories containing this gene/protein

DNA replication, essential genes

This gene is a member of the following regulons

Spo0A regulon

The DnaA regulon

The gene

Basic information

  • Locus tag: BSU00010

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: dnaA family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains: AAA+ domain
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
    • SirA displaces DnaA from the replication origin PubMed
    • YabA inhibits co-operative binding of DnaA to the oriC DNA PubMed
    • DnaA helix formation (and thus replication initiation) is inhibited by the interaction of Soj with the AAA+ domain of DnaA PubMed

Database entries

  • Structure:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Philippe Noirot, Jouy-en-Josas, France homepage

Peter Graumann, Freiburg University, Germany homepage

Alan Grossman, MIT, Cambridge, MA, USA

Your additional remarks

References

Reviews

The DnaA regulon

Original publications

Additional publications: PubMed

Retrieved from "http://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=159332"