Non-crystallographic symmetry in proteins: Jahn–Teller-like and Butterfly-like effects?

• Published in: Journal of biological inorganic chemistry 2019-02, Vol.24 (1), p.91-101
• Main Authors: Silva, José Malanho, Giuntini, Stefano, Cerofolini, Linda, Geraldes, Carlos F. G. C., Macedo, Anjos L., Ravera, Enrico, Fragai, Marco, Luchinat, Claudio, Calderone, Vito
• Format: Article
• Language: English
• Subjects: Asymmetry; Binding Sites; Biochemistry; Biomedical and Life Sciences; Carbonic anhydrase II; Carbonic Anhydrase II - chemistry; Crystallography; Crystallography, X-Ray; Crystals; Humans; Life Sciences; Microbiology; Models, Molecular; N-Terminus; Nickel; Nickel - chemistry; Original Paper; Protein Conformation; Symmetry
• ISSN: 0949-8257; 1432-1327
• DOI: 10.1007/s00775-018-1630-0

Partial symmetry, i.e., the presence of more than one molecule in the asymmetric unit of a crystal, is a relatively rare phenomenon in small-molecule crystallography, but is quite common in protein crystallography, where it is typically known as non-crystallographic symmetry (NCS). Several papers in literature propose molecular determinants such as crystal contacts, thermal factors, or TLS parameters as an explanation for the phenomenon of intrinsic asymmetry among molecules that are in principle equivalent. Nevertheless, are all of the above determinants the cause or are they rather the effect? In the general frame of the NCS often observed in crystals of biomolecules, this paper deals with nickel(II)-substituted human carbonic anhydrase(II) (hCAII) and its SAD structure determination at the nickel edge. The structure revealed two non-equivalent molecules in the asymmetric unit, the presence of a secondary nickel-binding site at the N-terminus of both molecules (which had never been found before in the nickel-substituted enzyme) and two different coordination geometries of the active site nickel (hexa-coordinated in one molecule and mainly penta-coordinated in the other). The above-mentioned standard molecular crystallographic determinants of this asymmetry are analyzed and presented in detail for this particular case. From these considerations, we speculate on the existence of a fundamental, although yet unknown, common cause for the partial symmetry that is so often encountered in X-ray structures of biomolecules.