4X2R
Crystal structure of PriA from Actinomyces urogenitalis
Summary for 4X2R
| Entry DOI | 10.2210/pdb4x2r/pdb |
| Descriptor | 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase, PHOSPHATE ION, 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID, ... (4 entities in total) |
| Functional Keywords | tim barrel, tryptophan/histidine synthesis, structural genomics, psi-biology, midwest center for structural genomics, mcsg, isomerase |
| Biological source | Actinomyces urogenitalis DSM 15434 |
| Total number of polymer chains | 1 |
| Total formula weight | 26510.30 |
| Authors | MICHALSKA, K.,VERDUZCO-CASTRO, E.A.,ENDRES, M.,BARONA-GOMEZ, F.,JOACHIMIAK, A.,Midwest Center for Structural Genomics (MCSG) (deposition date: 2014-11-26, release date: 2014-12-24, Last modification date: 2023-09-27) |
| Primary citation | Juarez-Vazquez, A.L.,Edirisinghe, J.N.,Verduzco-Castro, E.A.,Michalska, K.,Wu, C.,Noda-Garcia, L.,Babnigg, G.,Endres, M.,Medina-Ruiz, S.,Santoyo-Flores, J.,Carrillo-Tripp, M.,Ton-That, H.,Joachimiak, A.,Henry, C.S.,Barona-Gomez, F. Evolution of substrate specificity in a retained enzyme driven by gene loss. Elife, 6:-, 2017 Cited by PubMed Abstract: The connection between gene loss and the functional adaptation of retained proteins is still poorly understood. We apply phylogenomics and metabolic modeling to detect bacterial species that are evolving by gene loss, with the finding that Actinomycetaceae genomes from human cavities are undergoing sizable reductions, including loss of L-histidine and L-tryptophan biosynthesis. We observe that the dual-substrate phosphoribosyl isomerase A or gene, at which these pathways converge, appears to coevolve with the occurrence of and genes. Characterization of a dozen PriA homologs shows that these enzymes adapt from bifunctionality in the largest genomes, to a monofunctional, yet not necessarily specialized, inefficient form in genomes undergoing reduction. These functional changes are accomplished via mutations, which result from relaxation of purifying selection, in residues structurally mapped after sequence and X-ray structural analyses. Our results show how gene loss can drive the evolution of substrate specificity from retained enzymes. PubMed: 28362260DOI: 10.7554/eLife.22679 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.05 Å) |
Structure validation
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