8TJ1

Isoreticular, interpenetrating co-crystal of Replication Initiator Protein REPE54 and symmetrical expanded duplex (31mer) containing the cognate REPE54 sequence and an additional G-C rich sequence with 2 sticky base overhangs and 3' terminal phosphates and crosslinked with EDC.

Summary for 8TJ1

• Entry DOI: 10.2210/pdb8tj1/pdb
• Related: 7u6k
• Descriptor: DNA (5'-D(CP*CP*CP*GP*GP*AP*CP*CP*TP*GP*TP*GP*AP*CP*AP*AP*AP*TP*TP*GP*CP*CP*CP*TP*CP*AP*GP*AP*CP*GP*GP*A)-3')|, DNA (5'-D(GP*GP*CP*CP*GP*TP*CP*TP*GP*AP*GP*GP*GP*CP*AP*AP*TP*TP*TP*GP*TP*CP*AP*CP*AP*GP*GP*TP*CP*CP*GP*A)-3'), Replication initiation protein, ... (5 entities in total)
• Functional Keywords: replication initiator repe complex co-crystal, dna binding protein-dna complex, dna binding protein, dna binding protein/dna
• Biological source: Escherichia coli K-12; More
• Total number of polymer chains: 3
• Total formula weight: 50468.01

Authors

Orun, A.R.,Shields, E.T.,Shrestha, R.,Slaughter, C.K.,Snow, C.D. (deposition date: 2023-07-20, release date: 2023-08-02, Last modification date: 2024-11-06)

Primary citation

Orun, A.R.,Slaughter, C.K.,Shields, E.T.,Vajapayajula, A.,Jones, S.,Shrestha, R.,Snow, C.D.
Tuning Chemical DNA Ligation within DNA Crystals and Protein-DNA Cocrystals.
Acs Nanosci Au, 4:338-348, 2024

PubMed Abstract: Biomolecular crystals can serve as materials for a plethora of applications including precise guest entrapment. However, as grown, biomolecular crystals are fragile in solutions other than their growth conditions. For crystals to achieve their full potential as hosts for other molecules, crystals can be made stronger with bioconjugation. Building on our previous work using carbodiimide 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide (EDC) for chemical ligation, here, we investigate DNA junction architecture through sticky base overhang lengths and the role of scaffold proteins in cross-linking within two classes of biomolecular crystals: cocrystals of DNA-binding proteins and pure DNA crystals. Both crystal classes contain DNA junctions where DNA strands stack up end-to-end. Ligation yields were studied as a function of sticky base overhang length and terminal phosphorylation status. The best ligation performance for both crystal classes was achieved with longer sticky overhangs and terminal 3'phosphates. Notably, EDC chemical ligation was achieved in crystals with pore sizes too small for intracrystal transport of ligase enzyme. Postassembly cross-linking produced dramatic stability improvements for both DNA crystals and cocrystals in water and blood serum. The results presented may help crystals containing DNA achieve broader application utility, including as structural biology scaffolds.

PubMed: 39430379
DOI: 10.1021/acsnanoscienceau.4c00013

Experimental method

X-RAY DIFFRACTION (3.15 Å)