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bioRxiv · 10.1101/2025.03.26.645602

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

Kaur, G.·Horton, J. R.·Tzertzinis, G.·Zhou, J.·Schildkraut, I.·Cheng, X.
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Abstract

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 nucleotide, AMP, over the nucleoside, adenosine. To investigate the substrate selectivity of HPAMPD, we determined its structure in the apo form and in complex with the adenosine analogs pentostatin (2- deoxycoformycin) 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 {beta}1, (2) the loop between helices H and I, and (3) the end of strand {beta}5 and its adjacent loop. We engineered a chimeric deaminase by integrating these elements from HPAMPD into another related mollusk nucleoside adenosine deaminase, the A. californica 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 the methylated form, 6mAMP. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/645602v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@be415forg.highwire.dtl.DTLVardef@b5f7a5org.highwire.dtl.DTLVardef@957514org.highwire.dtl.DTLVardef@397e9a_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Kaur, G., Horton, J. R., Tzertzinis, G., Zhou, J., Schildkraut, I., Cheng, X.. 2025-03-27. Structural basis of substrate specificity of Helix pomatia AMP deaminase and a chimeric ADGF adenosine deaminase. https://doi.org/10.1101/2025.03.26.645602

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