7PU4
Crystal structure of the dimer RBP-N and RBP-Trunc from Thermotoga maritima Ribose Binding Protein
Summary for 7PU4
| Entry DOI | 10.2210/pdb7pu4/pdb |
| Descriptor | Ribose ABC transporter, periplasmic ribose-binding protein (3 entities in total) |
| Functional Keywords | periplasmic binding protein, substrate binding protein, ribose, ligand binding, sugar binding protein |
| Biological source | Thermotoga maritima MSB8 More |
| Total number of polymer chains | 4 |
| Total formula weight | 72792.68 |
| Authors | Romero-Romero, S.,Michel, F.,Hocker, B. (deposition date: 2021-09-28, release date: 2023-03-08, Last modification date: 2024-02-07) |
| Primary citation | Michel, F.,Romero-Romero, S.,Hocker, B. Retracing the evolution of a modern periplasmic binding protein. Protein Sci., :e4793-e4793, 2023 Cited by PubMed Abstract: Investigating the evolution of structural features in modern multidomain proteins helps to understand their immense diversity and functional versatility. The class of periplasmic binding proteins (PBPs) offers an opportunity to interrogate one of the main processes driving diversification: the duplication and fusion of protein sequences to generate new architectures. The symmetry of their two-lobed topology, their mechanism of binding, and the organization of their operon structure led to the hypothesis that PBPs arose through a duplication and fusion event of a single common ancestor. To investigate this claim, we set out to reverse the evolutionary process and recreate the structural equivalent of a single-lobed progenitor using ribose-binding protein (RBP) as our model. We found that this modern PBP can be deconstructed into its lobes, producing two proteins that represent possible progenitor halves. The isolated halves of RBP are well folded and monomeric proteins, albeit with a lower thermostability, and do not retain the original binding function. However, the two entities readily form a heterodimer in vitro and in-cell. The x-ray structure of the heterodimer closely resembles the parental protein. Moreover, the binding function is fully regained upon formation of the heterodimer with a ligand affinity similar to that observed in the modern RBP. This highlights how a duplication event could have given rise to a stable and functional PBP-like fold and provides insights into how more complex functional structures can evolve from simpler molecular components. PubMed: 37788980DOI: 10.1002/pro.4793 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.69 Å) |
Structure validation
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