5C2D

K428A mutant gp2c of large terminase subunit from bacteriophage sf6 with calcium

Summary for 5C2D

• Entry DOI: 10.2210/pdb5c2d/pdb
• Related: 4IDH 5C10 5C12 5C15 5C2F
• Descriptor: Gene 2 protein, CALCIUM ION (3 entities in total)
• Functional Keywords: nuclease domain, metal ion, metal binding protein
• Biological source: Enterobacteria phage Sf6 (Shigella flexneri bacteriophage VI)
• Total number of polymer chains: 1
• Total formula weight: 30761.66

Authors

Zhao, H.,Tang, L. (deposition date: 2015-06-15, release date: 2015-10-21, Last modification date: 2024-03-06)

Primary citation

Zhao, H.,Lin, Z.,Lynn, A.Y.,Varnado, B.,Beutler, J.A.,Murelli, R.P.,Le Grice, S.F.,Tang, L.
Two distinct modes of metal ion binding in the nuclease active site of a viral DNA-packaging terminase: insight into the two-metal-ion catalytic mechanism.
Nucleic Acids Res., 43:11003-11016, 2015

PubMed Abstract: Many dsDNA viruses encode DNA-packaging terminases, each containing a nuclease domain that resolves concatemeric DNA into genome-length units. Terminase nucleases resemble the RNase H-superfamily nucleotidyltransferases in folds, and share a two-metal-ion catalytic mechanism. Here we show that residue K428 of a bacteriophage terminase gp2 nuclease domain mediates binding of the metal cofactor Mg(2+). A K428A mutation allows visualization, at high resolution, of a metal ion binding mode with a coupled-octahedral configuration at the active site, exhibiting an unusually short metal-metal distance of 2.42 Å. Such proximity of the two metal ions may play an essential role in catalysis by generating a highly positive electrostatic niche to enable formation of the negatively charged pentacovalent phosphate transition state, and provides the structural basis for distinguishing Mg(2+) from Ca(2+). Using a metal ion chelator β-thujaplicinol as a molecular probe, we observed a second mode of metal ion binding at the active site, mimicking the DNA binding state. Arrangement of the active site residues differs drastically from those in RNase H-like nucleases, suggesting a drifting of the active site configuration during evolution. The two distinct metal ion binding modes unveiled mechanistic details of the two-metal-ion catalysis at atomic resolution.

PubMed: 26450964
DOI: 10.1093/nar/gkv1018

Experimental method

X-RAY DIFFRACTION (1.59 Å)