5ysp: Difference between revisions
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==Pyrophosphate-dependent kinase in the ribokinase family complexed with a pyrophosphate analog and myo-inositol== | |||
<StructureSection load='5ysp' size='340' side='right'caption='[[5ysp]], [[Resolution|resolution]] 1.70Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ysp]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermotoga_maritima_MSB8 Thermotoga maritima MSB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YSP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5YSP 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]] 1.7Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=MDN:METHYLENEDIPHOSPHONIC+ACID'>MDN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=5ysp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ysp OCA], [https://pdbe.org/5ysp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ysp RCSB], [https://www.ebi.ac.uk/pdbsum/5ysp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ysp ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/Q9WYP6_THEMA Q9WYP6_THEMA] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Almost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes. | |||
Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants.,Nagata R, Fujihashi M, Sato T, Atomi H, Miki K Nat Commun. 2018 May 2;9(1):1765. doi: 10.1038/s41467-018-04201-z. PMID:29720581<ref>PMID:29720581</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Fujihashi | <div class="pdbe-citations 5ysp" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Thermotoga maritima MSB8]] | |||
[[Category: Fujihashi M]] | |||
[[Category: Miki K]] | |||
[[Category: Nagata R]] | |||
