Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural insights into the exchange mechanism of a replicative DNA polymerase.
Journal, issue, pages	Nucleic Acids Res, Vol. 53, Issue 22, Year 2025
Publish date	Nov 26, 2025
Authors	Xiang Feng / Michelle M Spiering / Almeida Ruda de Luna Santos / Stephen J Benkovic / Huilin Li /
PubMed Abstract	Replicative DNA polymerases are distinguished by their speed, processivity, and fidelity. While speed and fidelity arise from the polymerase's intrinsic catalytic and proofreading activities, ...Replicative DNA polymerases are distinguished by their speed, processivity, and fidelity. While speed and fidelity arise from the polymerase's intrinsic catalytic and proofreading activities, processivity is typically attributed to the DNA sliding clamp that tethers the polymerase to DNA. However, additional mechanisms may also contribute. The T4 bacteriophage polymerase can exchange on-the-fly, a process likely contributing to its ∼10-fold higher synthesis rate compared with human polymerases. Here, we reconstituted the T4 holoenzyme and polymerase exchange complexes using purified gp43 polymerase, gp45 sliding clamp, and a primer-template DNA substrate. Cryo-electron microscopy (cryo-EM) analysis revealed either one or two polymerases bound to the clamp and DNA. In the one-polymerase complex, the DNA threads perpendicularly through the clamp, supporting processive synthesis. In contrast, the two-polymerase complex displays a markedly tilted DNA orientation, impeding sliding and representing exchange intermediates. Three distinct conformational states of the two-polymerase complex define a multistep exchange mechanism. To our knowledge, these findings provide the first molecular-level view of replicative polymerase exchange.
External links	Nucleic Acids Res / PubMed:41459747 / PubMed Central
Methods	EM (single particle)
Resolution	3.57 - 3.99 Å
Structure data	47531 9e5y EMDB-47531: T4 bacteriophage replicative holoenzyme, DNA in right Polymerase(State 1) PDB-9e5y: T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 1 Method: EM (single particle) / Resolution: 3.57 Å 47824 9ea2 EMDB-47824: T4 bacteriophage replicative holoenzyme, DNA in left Polymerase(State 2) PDB-9ea2: T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 2 Method: EM (single particle) / Resolution: 3.7 Å 47825 9ea3 EMDB-47825: T4 bacteriophage replicative holoenzyme with triple mutants D75R, Q430E, and K432E on exo- Polymerase PDB-9ea3: T4 bacteriophage replicative holoenzyme containing triple mutations D75R, Q430E, and K432E in the exonuclease-deficient polymerase Method: EM (single particle) / Resolution: 3.99 Å 47826 9ea6 EMDB-47826: T4 bacteriophage replicative holoenzyme, DNA in left Polymerase(State 3) PDB-9ea6: T4 Bacteriophage Replicative Polymerase Captured in Polymerase Exchange State 3 Method: EM (single particle) / Resolution: 3.74 Å
Chemicals	ChemComp-CA: Unknown entry ChemComp-D3T: 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE
Source	escherichia phage t4 (virus) synthetic construct (others)
Keywords	replication/DNA / replication / T4 / holoenzyme / replication-DNA complex / Transferase/DNA / Transferase-DNA complex