MetaCyc Enzyme: chloroplastic glyceraldehyde 3-phosphate dehydrogenase

Gene: GapA-1 Accession Number: AT3G26650 (MetaCyc)

Synonyms: gapA, GABA, GAPDH

Species: Arabidopsis thaliana col

Component of: chloroplastic glyceraldehyde 3-phosphate dehydrogenase/phosphoribulokinase (extended summary available)

Subunit composition of chloroplastic glyceraldehyde 3-phosphate dehydrogenase = [GapA-1]4
         chloroplastic glyceraldehyde 3-phosphate dehydrogenase A = GapA-1

The Arabidopsis thaliana gene GapA-1 encodes a glyceraldehyde 3-phosphate dehydrogenase (GAPDH). The gene was expressed in Escherichia coli and purified as a monomer. In vitro reconstitution of the GAPDH complex showed that the protein forms a tetramer of apparent mass of 120 kDa in the presence of NAD or NADP. Activity is higher in the presence of NADP [Marri05].

The protein is redox insensitive when treated with thioredoxin, and is inactivated by oxidized dithiothreitol and other oxidants, including hydrogen peroxide. This inactivation could not be reverted with reductants and is caused by an irreversible oxidation of Cys-149.

Locations: plastid stroma

Molecular Weight of Polypeptide: 36 kD (experimental) [Marri05 ]

Molecular Weight of Multimer: 120 kD (experimental) [Marri05]

Unification Links: ArrayExpress:P25856 , Entrez-gene:GABA , Entrez:BAB01730 , PhylomeDB:P25856 , Pride:P25856 , Protein Model Portal:P25856 , SMR:P25856 , String:P25856 , TAIR:AT3G26650 , UniProt:P25856

Relationship Links: Entrez-Nucleotide:PART-OF:AB026648 , InterPro:IN-FAMILY:IPR006424 , InterPro:IN-FAMILY:IPR016040 , InterPro:IN-FAMILY:IPR020828 , InterPro:IN-FAMILY:IPR020829 , InterPro:IN-FAMILY:IPR020830 , InterPro:IN-FAMILY:IPR020831 , Panther:IN-FAMILY:PTHR10836 , PDB:Structure:3K2B , PDB:Structure:3QV1 , PDB:Structure:3RVD , Pfam:IN-FAMILY:PF00044 , Pfam:IN-FAMILY:PF02800 , Prints:IN-FAMILY:PR00078 , Prosite:IN-FAMILY:PS00071 , Smart:IN-FAMILY:SM00846

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Cellular Component: GO:0009532 - plastid stroma

Created 11-Jan-2007 by Tissier C , TAIR

Enzymatic reaction of: glyceraldehyde-3-phosphate dehydrogenase (chloroplastic glyceraldehyde 3-phosphate dehydrogenase)

EC Number:

D-glyceraldehyde 3-phosphate + NADP+ + phosphate <=> 1,3-bisphospho-D-glycerate + NADPH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the Enzyme Commission system.

The reaction is favored in the opposite direction.

In Pathways: Calvin-Benson-Bassham cycle

This enzymatic activity is part of the Calvin cycle and is subject to redox-mediated regulation [Trost06].

Enzymatic reaction of: glyceraldehyde 3-phosphate dehydrogenase

EC Number:

D-glyceraldehyde 3-phosphate + NAD+ + phosphate <=> 1,3-bisphospho-D-glycerate + NADH + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

This reaction is reversible.

In Pathways: superpathway of anaerobic sucrose degradation , gluconeogenesis I , sucrose biosynthesis I (from photosynthesis) , glycolysis I (from glucose 6-phosphate)

The A4-GADPH protein complex has a much lower affinity for NADH, but, this enzymatic activity is not subject to redox-mediated regulation and may potentially play a part in dark metabolism in chloroplasts [Trost06, Pupillo73].

Subunit of: chloroplastic glyceraldehyde 3-phosphate dehydrogenase/phosphoribulokinase

Synonyms: GAPDH/CP12/PRK complex

Species: Arabidopsis thaliana col

Subunit composition of chloroplastic glyceraldehyde 3-phosphate dehydrogenase/phosphoribulokinase = [GapA-1]8[PRK]4[CP12-2]2
         chloroplastic glyceraldehyde 3-phosphate dehydrogenase A = GapA-1
         chloroplastic phosphoribulokinase = PRK
         CP12 subunit = CP12-2

This complex is largely inactive, and represents a way for plants and lower photosynthetic organisms to reversibly shut-down two important photosynthetic Calvin cycle enzymes in the dark, under oxidixing and NADH-rich conditions in the chloroplasts [Trost06].

Complexes have been described which contain both the protein catalyzing glyceraldehydes 3-phosphate dehydrogenase ( and phosphoribulokinase ( activities [Scheibe02, Marri05]. The GAPDH/CP12/PRK complex was reconstituted in vitro using purified recombinant proteins. In Arabidopsis thaliana GAPDH is encoded by two duplicated genes (GapA-1 and GapA-2), one PRK gene and two closely related genes (CP12-1 and CP12-2) and a third divergent one (CP12-3) [Marri05a]. The in vitro reconstitution was performed using GapA-1, PRK and CP12-2. GapA-1 and PRK are the two catalytic enzymes, whereas CP12 appears to play a regulatory role. The activity of both enzymes was drastically reduced in comparison to their more active form (see chloroplastic glyceraldehyde 3-phosphate dehydrogenase and phosphoribulokinase) [Marri05]. Within the complex PRK is 12-fold less active than the free oxidized version and 50-fold less active than the reduced enzyme. Similarly, the NADPH-dependent activity of GapA in the complex is 5-fold lower than for the free enzyme (the NADH-dependent activity remains unchanged) [Marri05]. The exact composition of the complex remains to be confirmed, although it has been tentatively proposed that it would contain two GapA tetramers (chloroplastic glyceraldehyde 3-phosphate dehydrogenase), two PRK dimers (phosphoribulokinase) and two CP12 [Marri05]. The complex appears to form first through the complexation GapA and CP12, followed by addition of PRK.

The holoproteins of this complex were tested as follows: GAPDH (GapA) either as an NADP or NAD complex, and CP12 and PRK either as reduced or oxidized proteins. No GAPDH/CP12/PRK complex formed when GapA was incubated with NADP and oxidized CP12 (note that although NADP dissociates the complex, it stimulates activity of chloroplastic glyceraldehyde 3-phosphate dehydrogenase). On the contrary, when NAD was used with oxidized CP12 the two subunits formed an apparent complex (this complex failed to form if NAD was used with reduced CP12) [Marri05]. PRK was unable to bind to CP12 under any redox conditions; however, oxidized PRK was able to form a supramolecular complex of about 640 kDa when incubated with GapA-NAD and oxidized CP12.

Molecular Weight: 640 kD (experimental) [Marri05]

Created 11-Jan-2007 by Tissier C , TAIR


Marri05: Marri L, Trost P, Pupillo P, Sparla F (2005). "Reconstitution and properties of the recombinant glyceraldehyde-3-phosphate dehydrogenase/CP12/phosphoribulokinase supramolecular complex of Arabidopsis." Plant Physiol 139(3);1433-43. PMID: 16258009

Marri05a: Marri L, Sparla F, Pupillo P, Trost P (2005). "Co-ordinated gene expression of photosynthetic glyceraldehyde-3-phosphate dehydrogenase, phosphoribulokinase, and CP12 in Arabidopsis thaliana." J Exp Bot 56(409);73-80. PMID: 15533878

Pupillo73: Pupillo P, Piccari GG (1973). "The effect of NADP on the subunit structure and activity of spinach chloroplast glyceraldehyde-3-phosphate dehydrogenase." Arch Biochem Biophys 154(1);324-31. PMID: 4144055

Scheibe02: Scheibe R, Wedel N, Vetter S, Emmerlich V, Sauermann SM (2002). "Co-existence of two regulatory NADP-glyceraldehyde 3-P dehydrogenase complexes in higher plant chloroplasts." Eur J Biochem 269(22);5617-24. PMID: 12423361

Trost06: Trost P, Fermani S, Marri L, Zaffagnini M, Falini G, Scagliarini S, Pupillo P, Sparla F (2006). "Thioredoxin-dependent regulation of photosynthetic glyceraldehyde-3-phosphate dehydrogenase: autonomous vs. CP12-dependent mechanisms." Photosynth Res 89(2-3);263-75. PMID: 17031544

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Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
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