8SCS
Bst DNA polymerase I Large Fragment wildtype D598A with 3'-amino primer, dGTP, and calcium time-resolved 8h
Summary for 8SCS
| Entry DOI | 10.2210/pdb8scs/pdb |
| Descriptor | DNA polymerase I, DNA primer/product, DNA template, ... (8 entities in total) |
| Functional Keywords | dna polymerase, np-dna, origin of life, time-resolved crystallography, replication-dna complex, replication/dna |
| Biological source | Geobacillus stearothermophilus More |
| Total number of polymer chains | 6 |
| Total formula weight | 148529.75 |
| Authors | Fang, Z.,Lelyveld, V.S.,Szostak, J.W. (deposition date: 2023-04-05, release date: 2023-10-25, Last modification date: 2023-11-08) |
| Primary citation | Lelyveld, V.S.,Fang, Z.,Szostak, J.W. Trivalent rare earth metal cofactors confer rapid NP-DNA polymerase activity. Science, 382:423-429, 2023 Cited by PubMed Abstract: A DNA polymerase with a single mutation and a divalent calcium cofactor catalyzes the synthesis of unnatural N3'→P5' phosphoramidate (NP) bonds to form NP-DNA. However, this template-directed phosphoryl transfer activity remains orders of magnitude slower than native phosphodiester synthesis. Here, we used time-resolved x-ray crystallography to show that NP-DNA synthesis proceeds with a single detectable calcium ion in the active site. Using insights from isotopic and elemental effects, we propose that one-metal-ion electrophilic substrate activation is inferior to the native two-metal-ion mechanism. We found that this deficiency in divalent activation could be ameliorated by trivalent rare earth and post-transition metal cations, substantially enhancing NP-DNA synthesis. Scandium(III), in particular, confers highly specific NP activity with kinetics enhanced by more than 100-fold over calcium(II), yielding NP-DNA strands up to 100 nucleotides in length. PubMed: 37883544DOI: 10.1126/science.adh5339 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
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