Structural basis for the substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase

Area of Science:

• Biochemistry
• Structural Biology
• Enzymology

Background:

• Helix pomatia AMP deaminase (HPAMPD) is an enzyme from mollusk foot muscle.
• HPAMPD is the first identified adenosine deaminase-related growth factor (ADGF) family member with a preference for adenosine monophosphate (AMP) over adenosine.
• Understanding substrate selectivity is crucial for enzyme function.

Purpose of the Study:

• To investigate the substrate selectivity of HPAMPD.
• To determine the structural basis for HPAMPD's preference for AMP.
• To explore the conservation of nucleotide-binding features in deaminases.

Main Methods:

• X-ray crystallography was used to determine the structure of HPAMPD in its apo form and complexed with pentostatin and pentostatin-5'-monophosphate.
• Structural comparison with human ADA2, another ADGF family member.
• Engineering of a chimeric deaminase by transferring key structural elements from HPAMPD to Aplysia ADGF.

Main Results:

• HPAMPD shares structural similarity with human ADA2 but possesses unique polar and charged residues in three specific regions that facilitate binding to the 5'-monophosphate group of AMP.
• The engineered chimeric enzyme demonstrated efficient AMP deamination while retaining adenosine deamination activity.
• The identified phosphate-binding feature is characteristic of nucleotide deaminases and is conserved across AMP and N6-methyl-AMP (6mAMP) deaminases.

Conclusions:

• HPAMPD's unique structural elements confer substrate specificity for AMP.
• The study provides insights into the evolution of substrate specificity within the ADGF family.
• The findings contribute to understanding the distinct substrate specificities of human adenosine deaminases for nucleosides, nucleotides, and methylated nucleotides.