6wup | pdb_00006wup

Crystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-5

spinqualitylabelsall models 6wup, resolution 1.49Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6wup is a 1 chain structure with sequence from Synthetic construct sequences. This structure supersedes the now removed PDB entry 6oki. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CL, EPE Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed Several enzymes are known to have evolved from non-catalytic proteins such as solute-binding proteins (SBPs). Although attention has been focused on how a binding site can evolve to become catalytic, an equally important question is: how do the structural dynamics of a binding protein change as it becomes an efficient enzyme? Here we performed a variety of experiments, including propargyl-DO3A-Gd(III) tagging and double electron-electron resonance (DEER) to study the rigid body protein dynamics of reconstructed evolutionary intermediates to determine how the conformational sampling of a protein changes along an evolutionary trajectory linking an arginine SBP to a cyclohexadienyl dehydratase (CDT). We observed that primitive dehydratases predominantly populate catalytically unproductive conformations that are vestiges of their ancestral SBP function. Non-productive conformational states, including a wide-open state, are frozen out of the conformational landscape via remote mutations, eventually leading to extant CDT that exclusively samples catalytically relevant compact states. These results show that remote mutations can reshape the global conformational landscape of an enzyme as a mechanism for increasing catalytic activity. Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme.,Kaczmarski JA, Mahawaththa MC, Feintuch A, Clifton BE, Adams LA, Goldfarb D, Otting G, Jackson CJ Nat Commun. 2020 Nov 23;11(1):5945. doi: 10.1038/s41467-020-19695-9. PMID:33230119 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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