View source for 31lr


==Crystal structure of Geobacillus thermodenitrificans YqeK in complex with a non-hydrolyzable Ap4A analog==
<StructureSection load='31lr' size='340' side='right'caption='[[31lr]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[31lr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Geobacillus_thermodenitrificans Geobacillus thermodenitrificans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=31LR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=31LR FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.4&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1KC6:[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]methyl]phosphinic+acid'>A1KC6</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=31lr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=31lr OCA], [https://pdbe.org/31lr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=31lr RCSB], [https://www.ebi.ac.uk/pdbsum/31lr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=31lr ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/A0ABY9QA59_GEOTD A0ABY9QA59_GEOTD] 
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Diadenosine tetraphosphate (Ap(4)A) and related dinucleoside tetraphosphates (Ap(4)Ns) are important stress-signaling molecules that coordinate bacterial adaptation to changing environmental conditions. Although the enzymes for turnover of Ap(4)A are known in several bacteria, the structural basis for substrate recognition and the cellular consequences of impaired Ap(4)A 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 Ap(4)A into two ADP molecules and removing Ap(4)A caps from RNA. The enzyme was active not only toward Ap(4)A but also toward the mixed dinucleotides Ap(4)G, Ap(4)C, and Ap(4)U in both in vitro and in vivo assays, hence acting as a broad-spectrum regulator of Ap(4)N 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 Ap(4)A 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 Ap(4)N recognition by HD-domain phosphohydrolases.

Molecular insights into the promiscuous Ap(4)N hydrolase YqeK.,Shivakumar RD, Happel N, Burchert F, Bruck M, Randau L, Pane-Farre J, Linne U, Freitag J, Hinrichs R, Kiontke S, Bange G, Bedrunka-Meinert P J Biol Chem. 2026 Aug 25;302(10):113490. doi: 10.1016/j.jbc.2026.113490. PMID:42641892<ref>PMID:42641892</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 31lr" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Geobacillus thermodenitrificans]]
[[Category: Large Structures]]
[[Category: Bange G]]
[[Category: Bedrunka P]]
[[Category: Kiontke S]]
[[Category: Shivakumar RD]]