Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' similar to N-acetylmuramoyl-L-alanine amidase <br/><br/>
+
* '''Description:''' malic enzyme <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'''
−
|''lytG''
+
|''maeA''  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yubE''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ywkA ''
 
|-
 
|-
 
|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''' || NAD-dependent malate dehydrogenase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || cell wall turnover
+
|style="background:#ABCDEF;" align="center"|'''Function''' || malate utilization 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 8.277  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 63 kDa, 4.883  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 846 bp, 282 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1746 bp, 582 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yubF]]'', ''[[yubD]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywkB]]'', ''[[tdk]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15090&#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:CAB15722&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:yubE_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:ywkA_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 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU31120
+
* '''Locus tag:''' BSU37050
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ywkAB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13954]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11312]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of 1,4-beta-linkages between N-acetyl-D-glucosamine and N-acetylmuramic acid residues in a peptidoglycan (according to Swiss-Prot)  
+
* '''Catalyzed reaction/ biological activity:''' (S)-malate + NAD<sup>+</sup> = pyruvate + CO<sub>2</sub> + NADH (according to Swiss-Prot) malate --> pyruvate
  
−
* '''Protein family:''' glycosyl hydrolase 73 family (according to Swiss-Prot)
+
* '''Protein family:''' malic enzymes family (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' [[MalS]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 72:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' secreted (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32083 O32083]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P45868 P45868]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU31120]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37050]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.1.1.38 1.1.1.38]
  
 
=== Additional information===
 
=== Additional information===
Line 88: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[maeA]]''-''[[ywkB]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' induced by malate ([[MalR]])
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' [[MalR]]: transcription activation
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 113: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 120:
 
=References=
 
=References=
  
−
<pubmed>17427287, </pubmed>
+
<pubmed>12949160, </pubmed>
−
# Horsburgh GJ, Atrih A, Williamson MP, Foster SJ. (2006) Dimeric structure of the cell shape protein MreC and its functional implications. ''Mol Microbiol.'' '''Dec;62(6):''' 1631-42. [http://www.ncbi.nlm.nih.gov/sites/entrez/17427287 PubMed]
+
# Doan, T., P. Servant, S. Tojo, H. Yamaguchi, G. Lerondel, K. Yoshida, Y. Fujita, and S. Aymerich. 2003. The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate. Microbiology 149: 2331-2343. [http://www.ncbi.nlm.nih.gov/sites/entrez/12949160 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 13:23, 8 June 2009

  • Description: malic enzyme

Gene name maeA
Synonyms ywkA
Essential no
Product NAD-dependent malate dehydrogenase
Function malate utilization
MW, pI 63 kDa, 4.883
Gene length, protein length 1746 bp, 582 aa
Immediate neighbours ywkB, tdk
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YwkA context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU37050

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: (S)-malate + NAD+ = pyruvate + CO2 + NADH (according to Swiss-Prot) malate --> pyruvate
  • Protein family: malic enzymes family (according to Swiss-Prot)
  • Paralogous protein(s): MalS

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: induced by malate (MalR)
  • Regulatory mechanism: MalR: transcription activation
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Stephane Aymerich, Microbiology and Molecular Genetics, INRA Paris-Grignon, France

Your additional remarks

References

Thierry Doan, Pascale Servant, Shigeo Tojo, Hirotake Yamaguchi, Guillaume Lerondel, Ken-Ichi Yoshida, Yasutaro Fujita, Stéphane Aymerich
The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate.
Microbiology (Reading): 2003, 149(Pt 9);2331-2343
[PubMed:12949160] [WorldCat.org] [DOI] (P p)

  1. Doan, T., P. Servant, S. Tojo, H. Yamaguchi, G. Lerondel, K. Yoshida, Y. Fujita, and S. Aymerich. 2003. The Bacillus subtilis ywkA gene encodes a malic enzyme and its transcription is activated by the YufL/YufM two-component system in response to malate. Microbiology 149: 2331-2343. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=88868"