9L14

Crystal structure of the monobody CL-1 in complex with the Escherichia coli adenylate kinase

Summary for 9L14

• Entry DOI: 10.2210/pdb9l14/pdb
• Descriptor: Adenylate kinase, Monobody CL-1, BIS(ADENOSINE)-5'-PENTAPHOSPHATE, ... (5 entities in total)
• Functional Keywords: monobody, adenylate kinase, conformational change, protein binding
• Biological source: Escherichia coli (strain K12); More
• Total number of polymer chains: 2
• Total formula weight: 34096.24

Authors

Nakamura, I.,Amesaka, H.,Tanaka, S.I.,Matsuo, T. (deposition date: 2024-12-13, release date: 2025-06-04)

Primary citation

Nakamura, I.,Amesaka, H.,Nagao, S.,Orito, N.,Negi, S.,Tanaka, S.I.,Matsuo, T.
Binding mechanism of adenylate kinase-specific monobodies.
Febs Lett., 2025

PubMed Abstract: Monobodies are synthetic antibody-mimetic proteins that regulate enzyme functions through protein-protein interactions. In this study, we investigated the binding mechanisms of monobodies to adenylate kinase (Adk). Calorimetric and X-ray crystallographic analyses revealed that CL-1, a monobody specific for the CLOSED form of Adk, binds to the CORE domain of Adk in an enthalpy-driven manner, forming several hydrogen bonds and a cation-π interaction at the protein interface, without perturbing the Adk backbone. In contrast, OP-4, an OPEN-form-specific monobody, exhibited entropy-driven binding. H-N 2D nuclear magnetic resonance (NMR), P-NMR, and calorimetric studies revealed conformational perturbations to Adk by OP-4, while substrate access remained intact. The different thermodynamic and structural effects between the monobodies highlight the diverse binding mechanisms among monobodies.

PubMed: 40400134
DOI: 10.1002/1873-3468.70076

Experimental method

X-RAY DIFFRACTION (1.86 Å)