Paramagnetic Solid-State NMR to Localize the Metal-Ion Cofactor in an Oligomeric DnaB Helicase

Paramagnetic metal ions can be inserted into ATP-fueled motor proteins by exchanging the diamagnetic Mg²⁺ cofactor with Mn²⁺ or Co²⁺ . Then, paramagnetic relaxation enhancement (PRE) or pseudo-contact shifts (PCSs) can be measured to report on the localization of the metal ion within the protein. We determine the metal position in the oligomeric bacterial DnaB helicase from Helicobacter pylori complexed with the transition-state ATP-analogue ADP:AlF₄ ^- and single-stranded DNA using solid-state NMR and a structure-calculation protocol employing CYANA. We discuss and compare the use of Mn²⁺ and Co²⁺ in localizing the ATP cofactor in large oligomeric protein assemblies. ³¹ P PCSs induced in the Co²⁺ -containing sample are then used to localize the DNA phosphate groups on the Co²⁺ PCS tensor surface enabling structural insights into DNA binding to the DnaB helicase.