9m8t: Difference between revisions
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==Crystal structure of the ribokinase RBK1 in complex with ADP from Saccharomyces cerevisiae== | |||
<StructureSection load='9m8t' size='340' side='right'caption='[[9m8t]], [[Resolution|resolution]] 2.66Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9m8t]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9M8T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9M8T 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]] 2.66Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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=9m8t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9m8t OCA], [https://pdbe.org/9m8t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9m8t RCSB], [https://www.ebi.ac.uk/pdbsum/9m8t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9m8t ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
ScRBK1 is a key enzyme responsible for the ATP-dependent phosphorylation of d-ribose, and plays a crucial role in many metabolic processes in S. cerevisiae. Herein, we demonstrate that ScRBK1 enzymatic activity is independently stimulated by monovalent cation and inorganic phosphate ion. We determined the crystal structures of ScRBK1-ADP and ScRBK1-d-ribose complexes. Each ScRBK1 monomer consists of a small lid domain and a large catalytic alpha/beta domain, exhibiting the typical structural characteristics of the carbohydrate kinase PfkB family. We mapped the critical interactions of ScRBK1 with ADP and d-ribose, as well as the activator monovalent cation. We identified key residues contributing to the enzymatic activity of ScRBK1, and elucidated the molecular mechanism underlying inorganic phosphate ion-dependent activation. Furthermore, our structural analyses highlighted the structural features, and interaction modes with both nucleotide and d-ribose substrates in HsRBK. Collectively, our study provides comprehensive structural and functional insights into the activation mechanisms of ScRBK1 by inorganic phosphate ion and monovalent cation, as well as the molecular mechanism of d-ribose phosphorylation, and reveals that HsRBK shares a common catalytic mechanism with RBK family members. | |||
Structural and biochemical insights into the molecular mechanism of ribokinase RBK1 from Saccharomyces cerevisiae.,Zhen S, Zhang Z, Fan Y, Li Y, Liu C, Guo F, Zhu Y, Wang Y, Zhang J, Xie J, Zhou H, Yang X, Liu X Int J Biol Macromol. 2025 Nov;331(Pt 1):148382. doi: , 10.1016/j.ijbiomac.2025.148382. Epub 2025 Oct 17. PMID:41110570<ref>PMID:41110570</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 9m8t" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Saccharomyces cerevisiae S288C]] | |||
[[Category: Liu XH]] | |||
[[Category: Yang XY]] | |||
