Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains

Abstract

Tandem duplications and fusions of single genes have led to magnificent expansions in the divergence of protein structures and functions over evolutionary timescales. One of the possible results is polydomain enzymes with interdomain cooperativities, few examples of which have been structurally characterized at the full-length level to explore their innate synergistic mechanisms. This work reports the crystal structures of a double-domain phosphagen kinase in both apo and ligand-bound states, revealing a novel asymmetric L-shaped arrangement of the two domains. Unexpectedly, the interdomain connections are not based on a flexible hinge linker but on a rigid secondary-structure element: a long α-helix that tethers the tandem domains in relatively fixed positions. Besides the connective helix, the two domains also contact each other directly and form an interdomain interface in which hydrogen bonds and hydrophobic interactions further stabilize the L-shaped domain arrangement. Molecular-dynamics simulations show that the interface is generally stable, suggesting that the asymmetric domain arrangement crystallographically observed in the present study is not a conformational state simply restrained by crystal-packing forces. It is possible that the asymmetrically arranged tandem domains could provide a structural basis for further studies of the interdomain synergy.

Biochemical and structural characterization of a novel arginine kinase from the spiderPolybetes pythagoricus

“…Structural characterization has been focused in both free-ligand and fully occupied active site of AK, that are called open and closed conformation, respectively ( Fernandez et al, 2007 ; Pruett et al, 2003 ; Zhou et al, 1998 ). Only, a few reports show structural details of binding of arginine in a binary complex, which is a crucial step during catalysis ( Lopez-Zavala et al, 2013 ; Wang et al, 2015 ). To date, horseshoe crab crystal structure has been reported for Chelicerate, which is comprised of more than 75,000 species ( Strong & Ellington, 1995 ).…”

Natural Products Containing ‘Rare’ Organophosphorus Functional Groups

“…Phosphagen kinases are enzymes that catalyze the reversible Mg 2+ -dependent transfer of the gamma phosphoryl group of ATP to a naturally occurring guanidino compounds, proto-phosphagens, such as creatine, glycocyamine, taurocyamine, lombricine, and arginine. Phosphagen kinases are a highly conserved family of proteins that nevertheless differ significantly with respect to their enzyme specificity and protein structure (monomeric, dimeric, and oligomeric forms of phophagen kinases are known) and distribution in the cell [59,60,61,62,63,64,65,66,67,68,69,70]. Among the most studied phosphagen kinases is the creatine kinase (EC 2.7.3.2), which is the only known phosphagen kinase to exist in vertebrates [71,72,73,74].…”