Glyceraldehyde-3-phosphate binding

Figure 2-13 (A) Stereoscopic view of the nucleotide binding domain of glyceraldehyde phosphate dehydrogenase. The enzyme is from Bacillus stearothermophilus but is homologous to the enzyme from animal sources. Residues are numbered 0-148. In this wire model all of the main chain C, O, and N atoms are shown but side chains have been omitted. The large central twisted P sheet, with strands roughly perpendicular to the page, is seen clearly hydrogen bonds are indicated by dashed lines. Helices are visible on both sides of the sheet. The coenzyme NAD+ is bound at the end of the P sheet toward the viewer. Note that the two phosphate groups in the center of the NAD+ are H-bonded to the N terminus of the helix beginning with RIO. From Skarzynski et al.llla (B) Structural formula for NAD+.

A similar conclusion was arrived at by Arnold and Pette ( 2) from studies carried out on the in vitro binding of aldolase glyceraldehyde phosphate dehyrogenase, fructose-6-phosphate kinase, phosphoglycerate kinase, pyruvate kinase and lactate dehydrogenase to the structural proteins F-actin, myosin, acto-myosin and stromaprotein. 

Modun, B. and Williams, P. (1999). The staphylococcal transferrin-binding protein is a cell wall glyceraldehyde-3-phosphate dehydrogenase, Infect. Immun., 67, 1086-1092. 

A three-substrate (A, B, and C), two-product (P and Q) enzyme reaction scheme in which all substrates and products bind and are released in an ordered fashion. Glyceraldehyde-3-phosphate dehydrogenase has been reported to have this reaction scheme. The steady-state and rapid equilibrium expressions, in the absence of products and abortive complexes, are identical to the ordered Ter Ter mechanism. See Ordered Ter Ter Mechanism... 

Glyceraldehyde-3-phosphate dehydrogenase is a homotetramer that carries out the oxidative phosphorylation of glyceraldehyde-3-phosphate into 1,3-bisphos- phoglycerate. During this reaction NADH is formed. Each subunit of the enzyme consists of two domains and has an NAD+ binding site. The N-terminal domain anchors the adenosine portion of the cofactor while the nicotinamide portion is involved in the catalytic reaction at the C-terminal domain. T brucei... 

The importance of binding energy to catalysis can be readily demonstrated. For example, the glycolytic enzyme triose phosphate isomerase catalyzes the interconversion of glyceraldehyde 3-phosphate and dihy-droxyacetone phosphate ... 

Figure 16.1 The binding of NAD+ to glyceraldehyde 3-phosphate dehydrogenase from Bacillus stearothermophilus. [From G. Biesecker, J. I. Harris, J. C. Thierry, J. E. Walker, and A. J. Wonacott, Nature, Lond. 266, 328 (1977).]...

The specificities of the enzymes are also nicely explained The enantiomers of the substrates of L-lactate and D-glyceraldehyde 3-phosphate dehydrogenases cannot be productively bound the hydrophobic pocket of alcohol dehydrogenase will not bind the charged side chains of lactate etc. However, we do not know if conformational changes occur during catalysis or if there is strain. 

The calculated free energy profile of the reaction catalyzed by triosephosphate isomerase. (Enz = enzyme DHAP = dihydroxyacetone phosphate GAP = glyceraldehyde-3-phosphate.) The free energy changes associated with binding of DHAP and GAP to the enzyme are calculated on the assumption that DHAP and GAP are present at concentrations of 40 /um. 

One of the major integral proteins of the erythrocyte membrane is the anion channel, or band-3 protein, which moves Cl- and HC03 anions across the membrane. The anion transporter has two identical subunits with molecular weights of about 95,000, and each subunit probably has 10 or 11 transmembrane helices. The band-3 protein is attached to the spectrin cytoskeleton through a smaller protein, anky-rin. The cytosolic domain of the anion transporter also binds the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase. 

Halophilic proteins whose solution structures are currently under study include glyceraldehyde-3-phosphate dehydrogenase from Hal-oarcula vallismortis (Krishnan and Altekar, 1990) and a heme-binding catalase-peroxidase from H.marismortui (F. Cendrin, H. Jouvre, and G. Zaccai, private communication). 

---