9DJR

T4 Lysozyme T115H/R119H/K147H/T151H co-crystallized with Cu(II)-NTA

Summary for 9DJR

• Entry DOI: 10.2210/pdb9djr/pdb
• Descriptor: Endolysin, COPPER (II) ION, NITRILOTRIACETIC ACID, ... (9 entities in total)
• Functional Keywords: hydrolase (o-glycosyl), double histidine mutation, dhis-cu(ii)-nta motif, lysozyme, hydrolase
• Biological source: Tequatrovirus T4
• Total number of polymer chains: 1
• Total formula weight: 19583.33

Authors

Besaw, J.E.,Ernst, O.P. (deposition date: 2024-09-06, release date: 2026-02-18, Last modification date: 2026-03-18)

Primary citation

Besaw, J.E.,Reichenwallner, J.,Chen, E.Y.,Hermet-Teesalu, P.,Tregubenko, A.,Kim, K.,Morizumi, T.,Ustav Jr., M.,Ernst, O.P.
Structural characterization of the Cu(II)-NTA spin label on alpha-helices by X-ray crystallography and electron paramagnetic resonance.
Structure, 2026

PubMed Abstract: Site-directed Cu(II)-labelling in pulsed electron paramagnetic resonance (EPR) spectroscopy has demonstrated narrow Cu(II)-Cu(II) distance distributions suitable to resolve subtle protein conformational changes. The high precision derives from a double histidine (dHis) mutation that effectively locks a Cu(II)-nitrilotriacetic acid (Cu(II)-NTA) moiety in place. To date, no structures featuring the dHis-Cu(II)-NTA motif have been resolved. This work presents the atomic-resolution X-ray crystal structures of seven α-helical dHis sites of T4 lysozyme (T4L) in the presence and absence of Cu(II)-NTA. Our research captured the rigid octahedral coordination of the dHis-Cu(II)-NTA complex as well as non-conventional binding modes, which provide valuable insight into dHis site selection. Pulsed EPR experiments on double dHis T4L mutants displayed remarkable agreement to the crystallography-derived distances. This research showcases the rigid configuration of the dHis-Cu(II)-NTA motif, providing geometric constraints that can be leveraged in modeling and molecular dynamics programs to extract protein structural details from EPR experiments.

PubMed: 41794029
DOI: 10.1016/j.str.2026.01.010

Experimental method

X-RAY DIFFRACTION (1.33 Å)