9XWQ

Phosphopantetheine adenylyltransferase loop-deletion mutant from psychrophilic methanotroph Methylocapsa palsarum

Summary for 9XWQ

• Entry DOI: 10.2210/pdb9xwq/pdb
• Descriptor: Phosphopantetheine adenylyltransferase (2 entities in total)
• Functional Keywords: phosphopantetheine adenylyltransferase loop deletion mutant, transferase
• Biological source: Methylocapsa palsarum
• Total number of polymer chains: 6
• Total formula weight: 112101.70

Authors

Nam, Y.,Hwang, J.,Do, H. (deposition date: 2025-11-28, release date: 2026-08-12)

Primary citation

Nam, Y.,Hwang, J.,Kim, B.,Lee, J.H.,Do, H.
A remote surface loop modulates core structure and cold activity in phosphopantetheine adenylyltransferase.
Plos One, 21:e0342296-e0342296, 2026

PubMed Abstract: Phosphopantetheine adenylyltransferase (PPAT), a key enzyme in the universal Coenzyme A biosynthetic pathway, is essential for cellular metabolism. However, the adaptive mechanisms of PPAT in psychrophilic (cold-adapted) organisms remain poorly understood. Here, we characterize PPAT from the psychrophilic methanotroph Methylocapsa palsarum (MpaPPAT). Sequence analysis identified a unique five-amino-acid insertion (SCRLS) within a surface-exposed loop, a feature conserved among psychrophilic homologues. To investigate its function, we determined the crystal structures of wild-type (WT) MpaPPAT and a loop-deletion mutant (MpaPPAT(Δ67-71)) and performed comparative biochemical analyses. Structurally, MpaPPAT forms a dimer-of-trimers hexamer. Biochemically, WT MpaPPAT maintains high catalytic activity at low temperatures (10-20 °C), whereas the MpaPPAT(Δ67-71) mutant exhibits impaired cold activity. The mutant structure reveals that the deletion of the distant surface loop induces a long-range allosteric change, resulting in a dual impairment: 1) a stabilization and rigidification ("clamping") of the central α-helix 4 (H4) at the hexameric core interface, and 2) a dramatic shift in the central pore's electrostatic potential from positive (WT) to negative (mutant). Our findings reveal that the SCRLS insertion is a critical allosteric modulator that provides a sophisticated dual mechanism for enzymatic cold adaptation. It maintains the conformational flexibility of the hexameric core, preventing the "clamping" effect, and simultaneously ensures a positively charged central channel to electrostatically steer negatively charged substrates (ATP and phosphopantetheine) into the active site, thereby overcoming the kinetic challenges of a low-temperature environment.

PubMed: 41818184
DOI: 10.1371/journal.pone.0342296

Experimental method

X-RAY DIFFRACTION (2.56 Å)