6ln3

Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP

spinqualitylabelsall models 6ln3, resolution 2.00Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6ln3 is a 1 chain structure with sequence from Aeropyrum pernix K1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2Å Ligands: AMP, ATP, CL, EPE, MG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function KADA_AERPE Publication Abstract from PubMed The crystal structure of an adenylate kinase from an extremophilic archaeon Aeropyrum pernix was determined in complex with full ligands, ATP-Mg2+ and AMP, at a resolution of 2.0 A. The protein forms a trimer as found for other adenylate kinases from archaea. Interestingly, the reacting three atoms, two phosphorus and one oxygen atoms, were located almost in line, supporting the SN2 nucleophilic substitution reaction mechanism. Based on the crystal structure obtained, the reaction coordinate was estimated by the quantum mechanics calculations combined with molecular dynamics. It was found that the reaction undergoes two energy barriers; the steps for breaking the bond between the oxygen and gamma-phosphorus atoms of ATP to produce a phosphoryl fragment and creating the bond between the phosphoryl fragment and the oxygen atom of the beta-phosphate group of ADP. The reaction coordinate analysis also suggested the role of amino acid residues for the catalysis of ADK. Crystal structure of adenylate kinase from an extremophilic archaeon Aeropyrum pernix with ATP and AMP.,Shibanuma Y, Nemoto N, Yamamoto N, Sampei GI, Kawai G J Biochem. 2020 Apr 9. pii: 5818497. doi: 10.1093/jb/mvaa043. PMID:32271910 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Adenylate kinase 3D structures

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