31LP

Crystal structure of Geobacillus thermodenitrificans YqeK

Summary for 31LP

• Entry DOI: 10.2210/pdb31lp/pdb
• Descriptor: bis(5'-nucleosyl)-tetraphosphatase (symmetrical), CALCIUM ION, ZINC ION, ... (4 entities in total)
• Functional Keywords: dinucleotides, ap4n, gram-positive bacteria, hydrolase
• Biological source: Geobacillus thermodenitrificans
• Total number of polymer chains: 1
• Total formula weight: 22704.57

Authors

Shivakumar, R.D.,Bedrunka, P.,Kiontke, S.,Bange, G. (deposition date: 2026-06-11, release date: 2026-10-07)

Primary citation

Shivakumar, R.D.,Happel, N.,Burchert, F.,Bruck, M.,Randau, L.,Pane-Farre, J.,Linne, U.,Freitag, J.,Hinrichs, R.,Kiontke, S.,Bange, G.,Bedrunka-Meinert, P.
Molecular insights into the promiscuous Ap 4 N hydrolase YqeK.
J.Biol.Chem., 302:113490-113490, 2026

PubMed Abstract: Diadenosine tetraphosphate (ApA) and related dinucleoside tetraphosphates (ApNs) are important stress-signaling molecules that coordinate bacterial adaptation to changing environmental conditions. Although the enzymes for turnover of ApA are known in several bacteria, the structural basis for substrate recognition and the cellular consequences of impaired ApA turnover remain poorly understood. Here, we characterize the Histidine-Aspartate (HD)-domain hydrolase YqeK from Bacillus subtilis. Deletion of yqeK impaired growth in stationary phase, sporulation, and biofilm formation, demonstrating a general role under nutrient limitation. YqeK forms a homodimer and functions as a manganese-dependent phosphohydrolase, symmetrically cleaving ApA into two ADP molecules and removing ApA caps from RNA. The enzyme was active not only toward ApA but also toward the mixed dinucleotides ApG, ApC, and ApU in both in vitro and in vivo assays, hence acting as a broad-spectrum regulator of ApN homeostasis. To understand this promiscuity, we determined crystal structures of YqeK in its apo- and ADP-bound state and in complex with a non-hydrolysable ApA analogue. The structures revealed an asymmetric recognition mechanism in which one nucleoside moiety and the proximal phosphate groups are tightly coordinated, whereas the distal nucleoside is accommodated largely through nonspecific interactions, explaining the ability of YqeK to process diverse substrates. Together, our findings establish YqeK as a central regulator of dinucleotide homeostasis and RNA metabolism and provide the structural framework for ApN recognition by HD-domain phosphohydrolases.

PubMed: 42641892
DOI: 10.1016/j.jbc.2026.113490

Experimental method

X-RAY DIFFRACTION (1.65 Å)