GapB

• 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: Cys, Met & Sulfate assimilation, Central C-metabolism
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 This image was kindly provided by SubtiList
Expression at a glance   PubMed

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

Database entries

• DBTBS entry: [1]

• SubtiList entry: [2]

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:

• Interactions:

• Localization: Cytoplasm (Homogeneous) PubMed

Database entries

• Structure: 3PRL (from B. halodurans)

• UniProt: O34425

• KEGG entry: [3]

• E.C. number: 1.2.1.59

Expression and regulation

• Operon: gapB-speD PubMed

• Expression browser: gapB PubMed

• Sigma factor: SigA PubMed

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

• Regulatory mechanism:
  • CcpN: transcription repression PubMed

• 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

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)