9R6U
Crystal structure of E. coli Adenylate kinase K47A mutant in complex with inhibitor Ap5A
Summary for 9R6U
| Entry DOI | 10.2210/pdb9r6u/pdb |
| Descriptor | Adenylate kinase, BIS(ADENOSINE)-5'-PENTAPHOSPHATE, GLYCEROL, ... (5 entities in total) |
| Functional Keywords | adenylate kinase, k47a mutant, ap5a, protein dynamics, transferase |
| Biological source | Escherichia coli |
| Total number of polymer chains | 2 |
| Total formula weight | 49071.67 |
| Authors | Phoeurk, C.,Wolf-Watz, M.,Sauer-Eriksson, A.E. (deposition date: 2025-05-13, release date: 2025-10-15, Last modification date: 2025-10-29) |
| Primary citation | Mattsson, J.,Phoeurk, C.,Schierholz, L.,Mushtaq, A.U.,Rodriguez Buitrago, J.A.,Rogne, P.,Sauer-Eriksson, A.E.,Wolf-Watz, M. Exploring Helical Fraying Linked to Dynamics and Catalysis in Adenylate Kinase. Biochemistry, 64:4281-4295, 2025 Cited by PubMed Abstract: Conformational dynamics is a fundamental aspect of enzymatic catalysis that, for example, can be linked to ligand binding and release, assembly of the active site, and the catalytic mechanism. The essential and metabolic enzyme adenylate kinase (AK) undergoes large-scale conformational changes in response to binding of its substrates ATP and AMP. As such, it has been intensely studied in search of linkages between dynamics and catalysis. For a complex conformational change to occur in a protein, whether it is of an induced fit or conformational selection nature, changes at several hinges are often required. Here, based on a comparative structure-function analysis of AK enzymes from and the archaea and from human AK1, we found that conformational changes in the enzymes are to a varying degree linked to bending, fraying, or unfolding/folding events of the termini of α-helices observed in various structural hot spots of the enzymes. The findings contribute with a mechanistic angle to how enzymatic dynamics and catalysis relate to the plasticity of the termini of α-helices. PubMed: 41042980DOI: 10.1021/acs.biochem.5c00306 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.77 Å) |
Structure validation
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