Catalytic pathway, substrate binding and stability in SAICAR synthetase: A structure and molecular dynamics study

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• De novo purine biosynthesis is crucial for cell viability and a target for drug development.
• Phosphoribosylaminoimidazole-succinocarboxamide (SAICAR) synthetase is a key enzyme in this pathway, catalyzing ATP-dependent ligation.
• Understanding SAICAR synthetase function is vital for designing novel antimicrobial and anticancer agents.

Purpose of the Study:

• To elucidate the structural basis of SAICAR synthetase activity using crystal structures and molecular dynamics.
• To investigate substrate binding, enzyme inhibition, and catalytic mechanisms.
• To provide insights for drug development targeting purine biosynthesis.

Main Methods:

• X-ray crystallography of Pyrococcus horikoshii SAICAR synthetase.
• Analysis of eight crystal structures with substrates and substrate mimics.
• Molecular dynamics simulations at 90°C.

Main Results:

• Crystal structures show minimal deviation from the apo form, with CAIR binding site preference for pyrimidine nucleotides.
• Aspartate (ASP) binding position clarified, and inhibition by CTP/UTP illustrated via CMP/UMP complexes.
• A phosphate ion in a complex suggests phosphorylation precedes aspartate attack, strengthening a proposed catalytic mechanism.

Conclusions:

• Structural data clarifies SAICAR synthetase substrate interactions and potential inhibition mechanisms.
• Molecular dynamics simulations reveal substrate binding strengths and the role of Mg2+ ions.
• Findings advance the understanding of de novo purine biosynthesis and inform drug discovery efforts.