Calcium-associated Pro367 ring puckering supports conformational selection in a thermophilic lipase
- 1Koc University
Abstract
Thermophilic bacterial lipases must combine structural stability with the conformational flexibility required for interfacial activation, yet the local organization of their metal-binding sites remains incompletely understood. Here, we determined two X-ray crystal structures of the family I.5 lipase from Geobacillus kaustophilus (GkLip). The 2.47-[A] orthorhombic model contains a Ca2+ ion at the conserved metal-binding site, whereas the 2.30-[A] anisotropic triclinic model contains four non-equivalent protein chains in which no Ca2+ ion was modeled. GkLip retains the canonical /{beta}-hydrolase fold, the Ser114-Asp318-His359 catalytic triad, the Phe17/Gln115 oxyanion-hole region, an extended lid, and a conserved Zn2+-binding site. In the orthorhombic structure, Gly287, Glu361, Asp366, and Pro367 contribute to the Ca2+ coordination environment. Pro367 adopts a C{gamma}-endo pucker in the Ca2+-containing structure; three Ca2+-free chains also adopt the endo pucker, whereas one adopts a C{gamma}-exo pucker. The presence of both Pro367 pucker states in the Ca2+-free structure is consistent with calcium preferentially stabilizing a pre-existing, coordination-compatible conformation. This local organization is further supported by an Arg35-centered network of direct and water-mediated contacts. Comparison with the 94%-identical open G. thermocatenulatus lipase reveals substantial lid rearrangement despite strong conservation of the protein core. Together, these structures highlight localized conformational variability at the calcium-binding region within an otherwise highly conserved thermophilic lipase scaffold.
Related
- DNA polymerase kappa supports repair-associated DNA synthesis and neuronal genome resilience
- OsVIPP1 Supports Rice Leaf Chloroplast Development and Is Associated with Seed Metabolic Changes and Yield-Related Traits
- Development of a CRISPR-Cas9 genome editing system for the extremely thermophilic bacterium Anaerocellum bescii
- Donor Aware Reanalysis of Neuronal Nuclei Supports STMN2 Depletion Associated with Nuclear TDP 43 loss in FTD and ALS
- Hypothalamic cell-type differences associated with selection for tameness in the silver fox
BibTeX
@misc{eyerci2026calciumassociated,
title = {{Calcium-associated Pro367 ring puckering supports conformational selection in a thermophilic lipase}},
author = {M. S. Eyerci and A. Tulek and F. I. Ozdemir and G. Sukur and H. Demirci},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.06.756949},
url = {https://www.biorxiv.org/content/10.64898/2026.10.06.756949v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Calcium-associated Pro367 ring puckering supports conformational selection in a thermophilic lipase
AU - M. S. Eyerci
AU - A. Tulek
AU - F. I. Ozdemir
AU - G. Sukur
AU - H. Demirci
PY - 2026
DA - 2026/10/06
PB - bioRxiv
DO - 10.64898/2026.10.06.756949
UR - https://www.biorxiv.org/content/10.64898/2026.10.06.756949v1
AB - Thermophilic bacterial lipases must combine structural stability with the conformational flexibility required for interfacial activation, yet the local organization of their metal-binding sites remains incompletely understood. Here, we determined two X-ray crystal structures of the family I.5 lipase from Geobacillus kaustophilus (GkLip). The 2.47-[A] orthorhombic model contains a Ca2+ ion at the conserved metal-binding site, whereas the 2.30-[A] anisotropic triclinic model contains four non-equivalent protein chains in which no Ca2+ ion was modeled. GkLip retains the canonical /{beta}-hydrolase fold, the Ser114-Asp318-His359 catalytic triad, the Phe17/Gln115 oxyanion-hole region, an extended lid, and a conserved Zn2+-binding site. In the orthorhombic structure, Gly287, Glu361, Asp366, and Pro367 contribute to the Ca2+ coordination environment. Pro367 adopts a C{gamma}-endo pucker in the Ca2+-containing structure; three Ca2+-free chains also adopt the endo pucker, whereas one adopts a C{gamma}-exo pucker. The presence of both Pro367 pucker states in the Ca2+-free structure is consistent with calcium preferentially stabilizing a pre-existing, coordination-compatible conformation. This local organization is further supported by an Arg35-centered network of direct and water-mediated contacts. Comparison with the 94%-identical open G. thermocatenulatus lipase reveals substantial lid rearrangement despite strong conservation of the protein core. Together, these structures highlight localized conformational variability at the calcium-binding region within an otherwise highly conserved thermophilic lipase scaffold.
ER -