Structural Insights into the N-Terminus and a Flexible P-x-P Loop near the Active Site of a Class III Aminotransferase

Abstract

Class III aminotransferases represent a structurally and functionally unique subgroup. However, the contribution of specific loop elements to their active-site architecture and cofactor-dependent structural transitions remain underexplored. We elucidated the structural framework underlying the catalytic function of class III fold Pyridoxal 5′-phosphate-dependent aminotransferase from the Antarctic bacterium Hymenobacter sp. PAMC 26554 (HyAT), and report its crystal structure at 2.31 Å resolution. The structure revealed a canonical class III fold organized as a functional homotetramer. Structural analysis identified a proline-containing motif (P-x-P) within the α10-α11 loop, which induces intrinsic disorder at the active-site entrance in the apo-form and revealed that a cooperative disorder-to-order transition is requisite for active-site assembly upon cofactor binding. We propose that this flexible loop region may be involved in modulating substrate access. Notably, this proline motif was conserved in homologs from Hyperthermophiles, despite the cold-adapted nature of HyAT. This convergence implies a common evolutionary strategy where the geometric constraints of proline are exploited to decouple local active-site dynamics from global scaffold stability, thereby addressing the stability–activity trade-off across diverse thermal environments. Our findings provide new molecular insights into the structural dynamics of class III aminotransferases and highlight evolutionary strategies for tuning enzyme flexibility in extreme environments.