Related Experiment Video
Updated: Aug 27, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
Structural landscape of a wide-open TPP: Insights into extreme conformational plasticity and allosteric potential
San Kim1, Karthik Rajan Rajamanickam2, Han-Gyeol Woo1
1Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea; Host-Directed Antiviral Research Center, Chonnam National University, Gwangju, 61186, Republic of Korea.
Abstract:
Trehalose-6-phosphate (T6P) homeostasis is a critical determinant of pathogen survival, positioning T6P phosphatase (TPP) as a high-priority antimicrobial target. Despite its significance, the development of universal TPP inhibitors has remained elusive. Here, we report the biochemical and structural characterization of Dermatophilus congolensis TPP (Dcon-TPP), which reveals a moderate catalytic turnover consistent with other bacterial orthologs. Our 2.9 Å crystal structure uncovers an unprecedented wide-open conformation in a state of functional disassembly, with the catalytic machinery sequestered across a ∼26 Å spatial gap. Comparative analysis reveals a remarkable ∼40 Å trajectory and 79° global rotation of the cap domain-the largest conformational rearrangement reported for the HAD superfamily to date. Our structure reveals that this extreme plasticity is linked to structural instability within the β8-strand, which likely acts as a mechanical latch to enable massive domain sweeps via a lever-arm mechanism. This inherent flexibility imposes a substantial entropic penalty on active-site pre-organization, providing a structural rationale for the modest catalytic efficiency shared by Group 3 TPPs. By elucidating this unique molecular switch, our findings suggest a cryptic allosteric site that can be targeted to lock the enzyme in an inert state, offering a promising strategy to overcome long-standing challenges in TPP inhibitor design.
Related Concept Videos
Ligand Binding and Linkage
Cooperative Allosteric Transitions
Cooperative Allosteric Transitions
Cooperative Allosteric Transitions
Allosteric Proteins-ATCase
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
