The structure of an engineered domain-swapped ribonuclease dimer and its implications for the evolution of proteins toward oligomerization.
BACKGROUND
Domain swapping has been proposed as a mechanism that explains the evolution from monomeric to oligomeric proteins. Bovine and human pancreatic ribonucleases are monomers with no biological properties other than their RNA cleavage ability. In contrast, the closely related bovine seminal ribonuclease is a natural domain-swapped dimer that has special biological properties, such as cytotoxicity to tumour cells. Several recombinant ribonuclease variants are domain-swapped dimers, but a structure of this kind has not yet been reported for the human enzyme.


RESULTS
The crystal structure at 2 A resolution of an engineered ribonuclease variant called PM8 reveals a new kind of domain-swapped dimer, based on the change of N-terminal domains between the two subunits. The swapping is fastened at both hinge peptides by the newly introduced Gln101, involved in two intermolecular hydrogen bonds and in a stacking interaction between residues of different chains. Two antiparallel salt bridges and water-mediated hydrogen bonds complete a new interface between subunits, while the hinge loop becomes organized in a 3(10) helix structure.


CONCLUSIONS
Proteins capable of domain swapping may quickly evolve toward an oligomeric form. As shown in the present structure, a single residue substitution reinforces the quaternary structure by forming an open interface. An evolutionary advantage derived from the new oligomeric state will fix the mutation and favour others, leading to a more extended complementary dimerization surface, until domain swapping is no longer necessary for dimer formation. The newly engineered swapped dimer reported here follows this hypothetical pathway for the rapid evolution of proteins.
Canals
A
A
Laboratori d'Enginyeria de Proteïnes, Facultat de Ciències, Universitat de Girona, Campus de Montilivi, Girona E-17071, Spain.
Pous
J
J
Guasch
A
A
Benito
A
A
Ribó
M
M
Vilanova
M
M
Coll
M
M
D000595:Amino Acid Sequence; D000818:Animals; D002417:Cattle; D018360:Crystallography, X-Ray; D019281:Dimerization; D004722:Endoribonucleases / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D004791:Enzyme Inhibitors / Q000737:chemistry; D019143:Evolution, Molecular; D006801:Humans; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D010446:Peptide Fragments / Q000737:chemistry / Q000235:genetics; D010926:Placental Hormones / Q000737:chemistry; D017434:Protein Structure, Tertiary / Q000235:genetics; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D012259:Ribonuclease, Pancreatic / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000235:genetics; D012260:Ribonucleases / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics
D004791:Enzyme Inhibitors; D010446:Peptide Fragments; D010926:Placental Hormones; D011506:Proteins; C022052:placental ribonuclease inhibitor; D004722:Endoribonucleases; D012260:Ribonucleases; C032523:ribonuclease SPL; D012259:Ribonuclease, Pancreatic