7O62
Crystal structure of a 2`-deoxyribosyltransferase from the psychrophilic bacterium Desulfotalea psychrophila.
Summary for 7O62
| Entry DOI | 10.2210/pdb7o62/pdb |
| Descriptor | Chains: A,B,C,D, GLYCEROL (3 entities in total) |
| Functional Keywords | psychrophilic enzyme, tetramer, thermal stability, transferase |
| Biological source | Desulfotalea psychrophila (strain LSv54 / DSM 12343) |
| Total number of polymer chains | 4 |
| Total formula weight | 67445.08 |
| Authors | Mancheno, J.M. (deposition date: 2021-04-09, release date: 2021-10-20, Last modification date: 2024-10-23) |
| Primary citation | Fernandez-Lucas, J.,Acebron, I.,Wu, R.Y.,Alfaro, Y.,Acosta, J.,Kaminski, P.A.,Arroyo, M.,Joachimiak, A.,Nocek, B.P.,De la Mata, I.,Mancheno, J.M. Biochemical and structural studies of two tetrameric nucleoside 2'-deoxyribosyltransferases from psychrophilic and mesophilic bacteria: Insights into cold-adaptation. Int.J.Biol.Macromol., 192:138-150, 2021 Cited by PubMed Abstract: Nucleoside 2'-deoxyribosyltransferases (NDTs) catalyze the cleavage of glycosidic bonds of 2'-deoxynucleosides and the following transfer of the 2'-deoxyribose moiety to acceptor nucleobases. Here, we report the crystal structures and biochemical properties of the first tetrameric NDTs: the type I NDT from the mesophilic bacterium Enterococcus faecalis V583 (EfPDT) and the type II NDT from the bacterium Desulfotalea psychrophila (DpNDT), the first psychrophilic NDT. This novel structural and biochemical data permitted an exhaustive comparative analysis aimed to shed light into the basis of the high global stability of the psychrophilic DpNDT, which has a higher melting temperature than EfPDT (58.5 °C versus 54.4 °C) or other mesophilic NDTs. DpNDT possesses a combination of unusual structural motifs not present neither in EfPDT nor any other NDT that most probably contribute to its global stability, in particular, a large aliphatic isoleucine-leucine-valine (ILV) bundle accompanied by a vicinal disulfide bridge and also an intersubunit disulfide bridge, the first described for an NDT. The functional and structural features of DpNDT do not fit the standard features of psychrophilic enzymes, which lead us to consider the implication of (sub)cellular levels together with the protein level in the adaptation of enzymatic activity to low temperatures. PubMed: 34624379DOI: 10.1016/j.ijbiomac.2021.09.164 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.4 Å) |
Structure validation
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