4JLD
Crystal Structures of adenylate kinase with 2 ADP's
Summary for 4JLD
| Entry DOI | 10.2210/pdb4jld/pdb |
| Related | 4JL5 4JL8 4JLA 4JLB 4JLO 4JLP |
| Descriptor | Adenylate kinase, ADENOSINE-5'-DIPHOSPHATE (3 entities in total) |
| Functional Keywords | transferase, adp binding, phosphoryl transfer reaction |
| Biological source | Aquifex aeolicus |
| Cellular location | Cytoplasm : O66490 |
| Total number of polymer chains | 2 |
| Total formula weight | 47674.43 |
| Authors | Cho, Y.-J.,Kern, D. (deposition date: 2013-03-12, release date: 2014-06-25, Last modification date: 2024-02-28) |
| Primary citation | Kerns, S.J.,Agafonov, R.V.,Cho, Y.J.,Pontiggia, F.,Otten, R.,Pachov, D.V.,Kutter, S.,Phung, L.A.,Murphy, P.N.,Thai, V.,Alber, T.,Hagan, M.F.,Kern, D. The energy landscape of adenylate kinase during catalysis. Nat.Struct.Mol.Biol., 22:124-131, 2015 Cited by PubMed Abstract: Kinases perform phosphoryl-transfer reactions in milliseconds; without enzymes, these reactions would take about 8,000 years under physiological conditions. Despite extensive studies, a comprehensive understanding of kinase energy landscapes, including both chemical and conformational steps, is lacking. Here we scrutinize the microscopic steps in the catalytic cycle of adenylate kinase, through a combination of NMR measurements during catalysis, pre-steady-state kinetics, molecular-dynamics simulations and crystallography of active complexes. We find that the Mg(2+) cofactor activates two distinct molecular events: phosphoryl transfer (>10(5)-fold) and lid opening (10(3)-fold). In contrast, mutation of an essential active site arginine decelerates phosphoryl transfer 10(3)-fold without substantially affecting lid opening. Our results highlight the importance of the entire energy landscape in catalysis and suggest that adenylate kinases have evolved to activate key processes simultaneously by precise placement of a single, charged and very abundant cofactor in a preorganized active site. PubMed: 25580578DOI: 10.1038/nsmb.2941 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.552 Å) |
Structure validation
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