PdhD

• Description: dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes
  
  

Gene name	pdhD
Synonyms	citL
Essential	no
Product	dihydrolipoamide dehydrogenase E3 subunit of both pyruvate dehydrogenase and 2-oxoglutarate dehydrogenase complexes
Function	links glycolysis and TCA cycle, enzyme in TCA cycle
Gene expression levels in SubtiExpress: pdhD
Interactions involving this protein in SubtInteract: PdhD
Metabolic function and regulation of this protein in SubtiPathways: pdhD
MW, pI	49 kDa, 4.76
Gene length, protein length	1410 bp, 470 aa
Immediate neighbours	pdhC, slp
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, most abundant proteins

This gene is a member of the following regulons

stringent response

The gene

Basic information

• Locus tag: BSU14610

Phenotypes of a mutant

• defects in sporulation and unable to grow on glucose as single carbon source PubMed

Database entries

• BsubCyc: BSU14610

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: Protein N(6)-(dihydrolipoyl)lysine + NAD⁺ = protein N(6)-(lipoyl)lysine + NADH (according to Swiss-Prot)

• Protein family: class-I pyridine nucleotide-disulfide oxidoreductase family (according to Swiss-Prot)

• Paralogous protein(s): AcoL, LpdV

Extended information on the protein

• Kinetic information: Michaelis-Menten PubMed

• Domains:

• Modification: phosphorylated (Ser/Thr/Tyr) PubMed

• Cofactors:

• Effectors of protein activity:
  • Inhibited thiamine 2-thiothiazolone diphosphate and NADH PubMed
  • Low sensibility to NADPH PubMed

• Interactions:
  • OdhA-OdhB-PdhD PubMed
  • PdhA-PdhB-PdhC-PdhD

• Localization: cytoplasm (according to Swiss-Prot)

Database entries

• BsubCyc: BSU14610

• Structure: 1EBD (complex with binding domain of dihydrolipoamide acetylase, Geobacillus stearothermophilus), 1EBD (complex with binding domain of dihydrolipoamide acetylase, Geobacillus stearothermophilus)

• UniProt: P21880

• KEGG entry: [3]

• E.C. number: 1.8.1.4

Expression and regulation

• • pdhA-pdhB-pdhC-pdhD PubMed
  • pdhC-pdhD PubMed

• Expression browser: pdhD PubMed

• Sigma factor:
  • pdhA: SigA PubMed
  • pdhC: SigA PubMed

• Regulation:
  • pdhA: expression activated by glucose (2.0-fold) PubMed
  • subject to negative stringent control upon amino acid limitation PubMed

• Regulatory mechanism:
  • stringent response: due to presence of guanine at +1 position of the transcript PubMed

• Additional information:
  • belongs to the 100 most abundant proteins PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium): 11483 PubMed
  • number of protein molecules per cell (complex medium with amino acids, without glucose): 30290 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 11794 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 8779 PubMed
  • number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 6741 PubMed

Biological materials

• Mutant:

• Expression vector:

• lacZ fusion: pGP723 (in pAC5), available in Stülke lab

• GFP fusion:

• two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

• Antibody:

• FLAG-tag construct: GP1427 (spc, based on pGP1331), available in the Stülke lab

References

Reviews

Kai Tittmann
Reaction mechanisms of thiamin diphosphate enzymes: redox reactions.
FEBS J: 2009, 276(9);2454-68
[PubMed:19476487] [WorldCat.org] [DOI] (I p)

K F Sheu, J P Blass
The alpha-ketoglutarate dehydrogenase complex.
Ann N Y Acad Sci: 1999, 893;61-78
[PubMed:10672230] [WorldCat.org] [DOI] (P p)

U Neveling, S Bringer-Meyer, H Sahm
Gene and subunit organization of bacterial pyruvate dehydrogenase complexes.
Biochim Biophys Acta: 1998, 1385(2);367-72
[PubMed:9655937] [WorldCat.org] [DOI] (P p)

M S Patel, T E Roche
Molecular biology and biochemistry of pyruvate dehydrogenase complexes.
FASEB J: 1990, 4(14);3224-33
[PubMed:2227213] [WorldCat.org] [DOI] (P p)

P A Frey
Mechanism of coupled electron and group transfer in Escherichia coli pyruvate dehydrogenase.
Ann N Y Acad Sci: 1982, 378;250-64
[PubMed:6805383] [WorldCat.org] [DOI] (P p)