Difference between revisions of "GapB"

From SubtiWiki
Jump to: navigation, search
Line 54: Line 54:
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29020&redirect=T BSU29020]
  
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gapB-speD.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gapB-speD.html]
Line 93: Line 94:
  
 
=== Database entries ===
 
=== Database entries ===
 +
* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU29020&redirect=T BSU29020]
  
 
* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=3PRL 3PRL] (from ''B. halodurans'')
 
* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=3PRL 3PRL] (from ''B. halodurans'')

Revision as of 14:29, 2 April 2014

  • Description: glyceraldehyde-3-phosphate dehydrogenase, NADP-dependent, gluconeogenic enzyme, forms a transhydrogenation cycle with GapA for balancing of NADPH

Gene name gapB
Synonyms ppc
Essential no
Product glyceraldehyde-3-phosphate dehydrogenase 2
Function anabolic enzyme in gluconeogenesis
Gene expression levels in SubtiExpress: gapB
Metabolic function and regulation of this protein in SubtiPathways:
gapB
MW, pI 37,3 kDa, 6.47
Gene length, protein length 1020 bp, 340 amino acids
Immediate neighbours speD, ytcD
Sequences Protein DNA DNA_with_flanks
Genetic context
GapB context.gif
This image was kindly provided by SubtiList
Expression at a glance   PubMed
GapB expression.png



















Categories containing this gene/protein

carbon core metabolism

This gene is a member of the following regulons

CcpN regulon

The gene

Basic information

  • Locus tag: BSU29020

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: D-glyceraldehyde 3-phosphate + phosphate + NAD(P)+ = 3-phospho-D-glyceroyl phosphate + NAD(P)H (according to Swiss-Prot)
    • This reaction is part of the gluconeogenesis
  • Protein family: glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)
  • Paralogous protein(s): GapA

Extended information on the protein

  • Kinetic information: Michaelis-Menten PubMed
  • Domains:
    • Nucleotid bindinge domain (12-13)
    • 2x Glyceraldehyde 3-phosphate binding domain (151-153) & (210-211)
  • Modification:
  • Cofactor(s): NADP+ (preferentially) and NAD+ PubMed
  • Effectors of protein activity:

Database entries

  • Structure: 3PRL (from B. halodurans)
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation:
    • repressed in the presence of glucose (70-fold) (CcpN) PubMed
    • strongly induced in response to glucose starvation in M9 medium PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
    • GP701 (gapB::spec), available in Stülke lab
    • 1A1004 ( gapB::erm), PubMed, available at BGSC
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • Antibody:

Labs working on this gene/protein

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

Your additional remarks

References

Imke G de Jong, Jan-Willem Veening, Oscar P Kuipers
Single cell analysis of gene expression patterns during carbon starvation in Bacillus subtilis reveals large phenotypic variation.
Environ Microbiol: 2012, 14(12);3110-21
[PubMed:23033921] [WorldCat.org] [DOI] (I p)

Martin Rühl, Dominique Le Coq, Stéphane Aymerich, Uwe Sauer
13C-flux analysis reveals NADPH-balancing transhydrogenation cycles in stationary phase of nitrogen-starving Bacillus subtilis.
J Biol Chem: 2012, 287(33);27959-70
[PubMed:22740702] [WorldCat.org] [DOI] (I p)

Matthew L Ferguson, Dominique Le Coq, Matthieu Jules, Stéphane Aymerich, Ovidiu Radulescu, Nathalie Declerck, Catherine A Royer
Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states.
Proc Natl Acad Sci U S A: 2012, 109(1);155-60
[PubMed:22190493] [WorldCat.org] [DOI] (I p)

Simon Tännler, Eliane Fischer, Dominique Le Coq, Thierry Doan, Emmanuel Jamet, Uwe Sauer, Stéphane Aymerich
CcpN controls central carbon fluxes in Bacillus subtilis.
J Bacteriol: 2008, 190(18);6178-87
[PubMed:18586936] [WorldCat.org] [DOI] (I p)

Helena B Thomaides, Ella J Davison, Lisa Burston, Hazel Johnson, David R Brown, Alison C Hunt, Jeffery Errington, Lloyd Czaplewski
Essential bacterial functions encoded by gene pairs.
J Bacteriol: 2007, 189(2);591-602
[PubMed:17114254] [WorldCat.org] [DOI] (P p)

Jean-Christophe Meile, Ling Juan Wu, S Dusko Ehrlich, Jeff Errington, Philippe Noirot
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.
Proteomics: 2006, 6(7);2135-46
[PubMed:16479537] [WorldCat.org] [DOI] (P p)

Pascale Servant, Dominique Le Coq, Stéphane Aymerich
CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes.
Mol Microbiol: 2005, 55(5);1435-51
[PubMed:15720552] [WorldCat.org] [DOI] (P p)

A Sekowska, J Y Coppée, J P Le Caer, I Martin-Verstraete, A Danchin
S-adenosylmethionine decarboxylase of Bacillus subtilis is closely related to archaebacterial counterparts.
Mol Microbiol: 2000, 36(5);1135-47
[PubMed:10844697] [WorldCat.org] [DOI] (P p)

S Fillinger, S Boschi-Muller, S Azza, E Dervyn, G Branlant, S Aymerich
Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium.
J Biol Chem: 2000, 275(19);14031-7
[PubMed:10799476] [WorldCat.org] [DOI] (P p)