NOTE: Some pages take a few seconds to load because of Chime Embeds. Please be patient after clicking on the structure (page 2) link!

Analysis of the Sulfolobus solfataricus glyceraldehyde 3-phosphate dehydrogenase: A Representative of the GAPDH-Like Family and the NAD-linked dehydrogenase class

Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is the enzyme that initiates the second (payoff) stage of glycolysis. GAPDH catalyzes the reaction that converts glyceraldehyde 3-phosphate (GAP) into 1,3 bisphosphoglycerate (1,3 BPG) (and the reverse reaction in gluconeogenesis). GAPDH oxidizes and phosphorylates GAP to produce 1,3 BPG. In this reaction, phosphorylation adds an inorganic phosphate to the carbony carbon of GAP, which also requires the oxidation of that carbonyl group (and reduction of NAD+ to NADH). Another enzyme catalyzes the reation of 1,3 BPG to 3-phosphoglycerate, producing an ATP molecule. After a few more steps, the 1,3 BPG becomes pyruvate. GAPDH has important functions beyond glycolysis.

Sulfolobus solfataricus is an aerobic crenarchaeon that grows optimally at 80 degrees C in pH 2 - 4 (cytoplasmic pH = 6.5) metabolizing suflur; it is considered to be a representative of a primordial organism. Crenarchaeons are part of the archaea superkingdom. Sulfolobales are hyperthermophilic archaea from terrestrial volcanic sites that grow in sulfur-rich hot acid springs. S solfataricus can grow either litoautotrophically by oxidizing sulfur or chemoheterotrophically on reduced carbon compounds (ie glycolysis).

NOTE: GAPDH in S. solfataricus reduces NAD+ or NADP+, with a slight preference for NADP+.

GAPDH is just about always a tetramer; for SS it is a homotetramer. Its rate of evolutionary change is one of the slowest known; nevertheless, there is not a great deal of sequence identity between archaea GAPDH and eukaryotic and eubacterial GAPDH. Yet, betweeen bacterial and eukaryotic GAPDH, there is a great deal of sequence identity. All GAPDH have a cysteine and a serine in their active sites. The reaction catalyzed goes through a thioester bond; a cysteine in the active site is responsible for forming this bond. The protein itself has two domains, a nucleotide (NAD+/NAPD+) binding domain and a catalytic domain with a large antiparallel beta sheet. Since it is in a thermophilic organism, the protein has been stabilized by ion clusters, salt bridges, and disulfide bonds to provide extra stability at high temperatures.

Resources Used:
NCBI (BLAST, Entrez, Taxonomy, OMIM, PubMed

PDB

EBI - FASTA, SWISS-PROT, TrEMBL, PROSITE, etc.

Predict Protein

SCOP

CATH

Databases and Tools for 3-D Protein Structure Comparison and Alignment

http://www.temple.edu/csar/pages/sirover.htm

http://archneur.ama-assn.org/issues/v55n10/abs/noc7618.html

http://www.mcis.duke.edu/cgi-bin/fps/getPerson.pl?personid=262

Isupov MN, et al. "Crystal structure of the glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeon Sulfolobus
solfataricus" J Mol Biol 1999 Aug 20;291(3):651-60.

http://www.bio.cmu.edu/Courses/BiochemMols/Glycolysis/

Cardon, Jeffrey W. Probes of catalytic cooperativity in glyceraldehyde 3-phosphate dehydrogenase. 1979

Other resources were used, too.