D-glyceraldehyde-3-phosphate dehydrogenase: three-dimensional structure and evolutionary significance

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) is a key enzyme in glycolysis.
• Understanding enzyme structure provides insights into catalytic mechanisms and evolutionary relationships.

Purpose of the Study:

• To determine the 3.0-Å resolution electron density map of lobster glyceraldehyde-3-phosphate dehydrogenase.
• To analyze the coenzyme (NAD) binding site and compare the enzyme's structure to other dehydrogenases.

Main Methods:

• Computation of a 3.0-Å resolution electron density map.
• Improvement of the map using single isomorphous replacement and subunit averaging techniques.

Main Results:

• The electron density map of lobster glyceraldehyde-3-phosphate dehydrogenase was successfully computed and improved.
• Nicotinamide adenine dinucleotide (NAD) was observed to bind in an open conformation near subunit interfaces.
• The coenzyme binding domain exhibits structural similarity to that of lactate dehydrogenase.

Conclusions:

• The observed structural fold in nucleotide-coenzyme-binding enzymes may represent a fundamental primordial element.
• This finding suggests a conserved evolutionary origin for enzymes utilizing nucleotide coenzymes.