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Abstract

Domains are the structural building blocks of proteins capable of autonomous folding. Their modular recombination gives rise to proteins with different functions. We identified an archaeal protein family, which contains a β-clam domain in context not of a AAA protein but of a C-terminal domain that has no significant sequence similarity to known domains. Here, we present the biochemical and crystallographic characterization of open reading frame number 1500 from Pyrococcus horikoshii, revealing that the C-domain forms a homohexameric twelve-bladed β-propeller, which we therefore name HP12 (homohexameric propeller with 12 blades). The structural similarity of the blades of HP12 to the superfamily of WD40-repeat propellers (RMSD < 1.8 Å over 70 residues), and structure-based sequence alignments substantiate a homologous relationship to β-propellers. Additionally, the two blades of a monomer have retained traces of an ancient duplication event, suggesting that fully amplified monomeric β-propellers evolved via oligomeric intermediates encoded by single-bladed ancestors. This supports our scenario that folded domains themselves arose by repetition and recombination of a set of ancestral peptides, one of which is the four-stranded β-meander corresponding to a propeller blade. Furthermore, we show that HP12 forms a ternary complex with a translationally coupled type III endonuclease and DNA implying a function in base excision repair. Because HP12 resembles DNA sliding clamps in pore size, charge distribution, and symmetry, we propose that HP12 is a PCNA analog. The ability of HP12 to encircle DNA provides a functional reason for the evolution of this oligomeric propeller with the, to our knowledge, largest number of blades and size of the central pore among all β-propellers characterized so far. This work was funded by the Max Planck Society (to ANL). (PAS) into a phosphonate monoester hydrolase (PMH). Three rounds of neutral drift, followed by six rounds of selection for improved promiscuous activity resulted in 110 000-fold increase of PMH activity (kcat/KM= 1.6x103 M-1 s-1) whereas the native sulfatase activity only decreased by 400-fold (kcat/KM= 5.9x104 M-1 s-1). Moreover the promiscuous hydrolysis of phosphate diesters also improved by 16-fold (kcat/KM = 1.3x105M-1 s-1); thus the evolved variant became a highly efficient promiscuous enzyme. Mutational analysis revealed the clustering of substitutions in loops that are originally absent in known PMH structures. Based on this lead, selections from semi-rationally designed loop-deletion libraries identified mutants tolerating up to 18 amino acids deletions and exhibiting altered specificity toward phosphonate monoesters. Structural and kinetic analysis of the evolutionary intermediates is providing insights into how these mutations triggered a switch in catalytic efficiency and specificity. Our results underline the versatility of promiscuous enzymes and their ability to quickly evolve a new activity via distinct mutational paths, including substitutions, insertions and deletions.This work is supported by the EU Marie-Curie networks ProSA and ENEFP.