9NTH

Helix pomatia AMP deaminase (HPAMPD) in complex with Pentostatin monophosphate (PMP)

This is a non-PDB format compatible entry.

Summary for 9NTH

• Entry DOI: 10.2210/pdb9nth/pdb
• Descriptor: AMP Deaminase, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 1,2-ETHANEDIOL, ... (10 entities in total)
• Functional Keywords: helix pomatia amp deaminase (hpampd); adenosine deaminase 2 (ada2); hydrolase; adenosine 5'-monophosphate deaminase; deoxycoformycin, hydrolase
• Biological source: Helix pomatia
• Total number of polymer chains: 4
• Total formula weight: 258322.10

Authors

Kaur, G.,Horton, J.R.,Cheng, X. (deposition date: 2025-03-18, release date: 2025-06-18, Last modification date: 2025-06-25)

Primary citation

Kaur, G.,Horton, J.R.,Tzertzinis, G.,Zhou, J.,Schildkraut, I.,Cheng, X.
Structural basis for the substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase.
J.Biol.Chem., :110357-110357, 2025

PubMed Abstract: Helix pomatia AMP deaminase (HPAMPD), an enzyme enriched in the foot muscle of the mollusk Helix pomatia, exhibits deaminase activity on adenosine-5'-monophosphate (AMP). HPAMPD is the first member of the adenosine deaminase-related growth factor (ADGF) family to prefer the nucleotideAMP over the nucleoside adenosine. To investigate the substrate selectivity of HPAMPD, we determined its structure in both the apo form and in complex with the adenosine analogs pentostatin and pentostatin-5'-monophosphate. Structurally, HPAMPD adopts a fold similar to human ADA2, an ADGF family member. HPAMPD has acquired the ability to interact with the 5'-monophosphate group of AMP through polar and charged residues located in three key structural elements: (1) the loop immediately following strand β1; (2) the loop between helices αH and αI; and (3) the end of strand β5 and its adjacent loop. We engineered a chimeric deaminase by integrating these elements from HPAMPD into another related mollusk nucleoside adenosine deaminase, Aplysia ADGF. The chimeric enzyme efficiently deaminates AMP, demonstrating a gained substrate specificity, while retaining the adenosine deamination activity of Aplysia ADGF. The phosphate-binding feature of HPAMPD is a hallmark of nucleotide deaminases, conserved among AMP and N6-methyl-AMP (6mAMP) deaminases. We discuss the human adenosine deaminases each with distinct substrate specificities for the nucleoside, the nucleotide (AMP), and its methylated form, 6mAMP.

PubMed: 40505866
DOI: 10.1016/j.jbc.2025.110357

Experimental method

X-RAY DIFFRACTION (1.61 Å)