Summary for 3M10
| Entry DOI | 10.2210/pdb3m10/pdb |
| Related | 1M15 1M80 |
| Descriptor | Arginine kinase, SULFATE ION (3 entities in total) |
| Functional Keywords | alpha-beta, atp-binding, kinase, nucleotide-binding, guanidino kinase, phosphagen kinase, transferase |
| Biological source | Limulus polyphemus (Atlantic horseshoe crab) |
| Total number of polymer chains | 2 |
| Total formula weight | 80691.64 |
| Authors | Yousef, M.S.,Clark, S.A.,Pruett, P.K.,Somasundaram, T.,Ellington, W.R.,Chapman, M.S. (deposition date: 2010-03-03, release date: 2010-03-16, Last modification date: 2023-09-06) |
| Primary citation | Niu, X.,Bruschweiler-Li, L.,Davulcu, O.,Skalicky, J.J.,Bruschweiler, R.,Chapman, M.S. Arginine kinase: joint crystallographic and NMR RDC analyses link substrate-associated motions to intrinsic flexibility. J.Mol.Biol., 405:479-496, 2011 Cited by PubMed Abstract: The phosphagen kinase family, including creatine and arginine kinases (AKs), catalyzes the reversible transfer of a "high-energy" phosphate between ATP and a phosphoguanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of AK structures were interpreted as a plastic deformation. Here, the structure of Limulus substrate-free AK is refined against high-resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa) and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.7 Å transition-state analog complex shows large substrate-induced domain motions that can be broken down into movements of smaller quasi-rigid bodies. The solution-state structure of substrate-free AK is most consistent with an equilibrium of substrate-free and substrate-bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, "substrate-induced" motions are along modes that are intrinsically flexible in the substrate-free enzyme and likely involve some degree of conformational selection. PubMed: 21075117DOI: 10.1016/j.jmb.2010.11.007 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.727 Å) |
Structure validation
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