9BKW

Crystal structure of a C2 domain from Trichomonas vaginalis

Summary for 9BKW

• Entry DOI: 10.2210/pdb9bkw/pdb
• Descriptor: XYPPX repeat family protein (2 entities in total)
• Functional Keywords: ssgcid, structural genomics, seattle structural genomics center for infectious disease, trichomonas vaginalis, c2 domain, lipid binding protein
• Biological source: Trichomonas vaginalis G3
• Total number of polymer chains: 1
• Total formula weight: 15905.21

Authors

Seattle Structural Genomics Center for Infectious Disease,Seattle Structural Genomics Center for Infectious Disease (SSGCID) (deposition date: 2024-04-29, release date: 2024-05-08, Last modification date: 2025-12-24)

Primary citation

Buchko, G.W.,Liu, L.,Battaile, K.P.,Craig, J.K.,Harmon, E.K.,Van Voorhis, W.C.,Myler, P.J.,Lovell, S.
A Trichomonas vaginalis C2-XYPPX-repeat protein with a structured C2 domain displaying dampened flexibility upon binding calcium.
Biochimie, 241:44-55, 2025

PubMed Abstract: C2 domains are ubiquitous membrane-binding modules of ∼130 residues in eukaryotes that are often associated with proteins involved in membrane trafficking and lipid modification. The genome of Trichomonas vaginalis, the most common, non-viral, sexually transmitted human pathogen, encodes eight genes that contain a N-terminal C2 module linked to a XYPPX-repeat domain of more than four XYPPX repeats (C2-XYPPX). While the function of the XYPPX-repeat domain remains unknown, its multiple association with C2 domains in T. vaginalis suggests it is important. The C2 domain from one of these C2-XYPPX-repeat proteins, Tv-C2-1, was structurally and physically characterized using X-ray crystallography and NMR spectroscopy. The crystal structure for Tv-C2-1 shows that this domain shares a fold common to all C2 domains, a compact Greek-key motif composed of eight anti-parallel β-strands in the type-2 topology. An NMR chemical shift perturbation study with Ca showed that Tv-C2-1 bound two Ca atoms primarily via two loops (loop-1 and loop-3) on the predicted calcium binding face of the protein with Ks of 58.0 ± 0.1 μM and 232 ± 6 μM. Estimations of the overall rotational correlation time, τ, in the apo (11.1 ns) and Ca-bound (9.2 ns) state suggests the protein becomes more compact upon Ca binding, consistent with a decrease in dynamics in loop-3 and marginally in loop-1 suggested by amide N heteronuclear steady-state {H}-N NOEs. Showing Tv-C2-1 binds calcium and adopts a compact Greek-key motif structure, two primary features of C2 domains, suggests understanding the function of the XYPPX-repeat domain may be warranted.

PubMed: 41285221
DOI: 10.1016/j.biochi.2025.11.011

Experimental method

X-RAY DIFFRACTION (1.85 Å)