6zjd

Crystal structure of human adenylate kinase 3, AK3, in complex with inhibitor ATP

spinqualitylabelsall models 6zjd, resolution 1.75Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6zjd is a 1 chain structure with sequence from Homo sapiens. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.75Å Ligands: ATP, CL, MG, NA Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function KAD3_HUMAN Publication Abstract from PubMed ATP and GTP are exceptionally important molecules in biology with multiple, and often discrete, functions. Therefore, enzymes that bind to either of them must develop robust mechanisms to selectively utilize one or the other. Here, this specific problem is addressed by molecular studies of the human NMP kinase AK3, which uses GTP to phosphorylate AMP. AK3 plays an important role in the citric acid cycle, where it is responsible for GTP/GDP recycling. By combining a structural biology approach with functional experiments, we present a comprehensive structural and mechanistic understanding of the enzyme. We discovered that AK3 functions by recruitment of GTP to the active site, while ATP is rejected and nonproductively bound to the AMP binding site. Consequently, ATP acts as an inhibitor with respect to GTP and AMP. The overall features with specific recognition of the correct substrate and nonproductive binding by the incorrect substrate bear a strong similarity to previous findings for the ATP specific NMP kinase adenylate kinase. Taken together, we are now able to provide the fundamental principles for GTP and ATP selectivity in the large NMP kinase family. As a side-result originating from nonlinearity of chemical shifts in GTP and ATP titrations, we find that protein surfaces offer a general and weak binding affinity for both GTP and ATP. These nonspecific interactions likely act to lower the available intracellular GTP and ATP concentrations and may have driven evolution of the Michaelis constants of NMP kinases accordingly. Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3.,Rogne P, Dulko-Smith B, Goodman J, Rosselin M, Grundstrom C, Hedberg C, Nam K, Sauer-Eriksson AE, Wolf-Watz M Biochemistry. 2020 Sep 11. doi: 10.1021/acs.biochem.0c00549. PMID:32822537 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See Also Adenylate kinase 3D structures

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