5ldb: Difference between revisions

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 ==Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ADP==
-<StructureSection load='5ldb' size='340' side='right' caption='[[5ldb]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5ldb' size='340' side='right'caption='[[5ldb]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5ldb]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Meiothermus_ruber_h328 Meiothermus ruber h328]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDB OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5LDB FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5ldb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Meiothermus_ruber_H328 Meiothermus ruber H328]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LDB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LDB FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ADP:ADENOSINE-5-DIPHOSPHATE'>ADP</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MrH_2468 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1297799 Meiothermus ruber H328])</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=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldb OCA], [http://pdbe.org/5ldb PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ldb RCSB], [http://www.ebi.ac.uk/pdbsum/5ldb PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldb ProSAT]</span></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=5ldb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ldb OCA], [https://pdbe.org/5ldb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ldb RCSB], [https://www.ebi.ac.uk/pdbsum/5ldb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ldb ProSAT]</span></td></tr>
 </table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Inorganic polyphosphate is a ubiquitous, linear biopolymer built of up to thousands of phosphate residues that are linked by energy-rich phosphoanhydride bonds. Polyphosphate kinases of the family 2 (PPK2) use polyphosphate to catalyze the reversible phosphorylation of nucleotide phosphates and are highly relevant as targets for new pharmaceutical compounds and as biocatalysts for cofactor regeneration. PPK2s can be classified based on their preference for nucleoside mono- or diphosphates or both. The detailed mechanism of PPK2s and the molecular basis for their substrate preference is unclear, which is mainly due to the lack of high-resolution structures with substrates or substrate analogs. Here, we report the structural analysis and comparison of a class I PPK2 (ADP-phosphorylating) and a class III PPK2 (AMP- and ADP-phosphorylating), both complexed with polyphosphate and/or nucleotide substrates. Together with complementary biochemical analyses, these define the molecular basis of nucleotide specificity and are consistent with a Mg(2+) catalyzed in-line phosphoryl transfer mechanism. This mechanistic insight will guide the development of PPK2 inhibitors as potential antibacterials or genetically modified PPK2s that phosphorylate alternative substrates.
+Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures.,Parnell AE, Mordhorst S, Kemper F, Giurrandino M, Prince JP, Schwarzer NJ, Hofer A, Wohlwend D, Jessen HJ, Gerhardt S, Einsle O, Oyston PCF, Andexer JN, Roach PL Proc Natl Acad Sci U S A. 2018 Mar 12. pii: 1710741115. doi:, 10.1073/pnas.1710741115. PMID:29531036<ref>PMID:29531036</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 5ldb" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Phosphotransferase|Phosphotransferase]]
+*[[Phosphotransferase 3D structures|Phosphotransferase 3D structures]]
+== References ==
+<references/>
 __TOC__
 </StructureSection>
-[[Category: Meiothermus ruber h328]]
+[[Category: Large Structures]]
-[[Category: Einsle, O]]
+[[Category: Meiothermus ruber H328]]
-[[Category: Gerhardt, S]]
+[[Category: Einsle O]]
-[[Category: Kemper, F]]
+[[Category: Gerhardt S]]
-[[Category: Schwarzer, N]]
+[[Category: Kemper F]]
-[[Category: Polyphosphate kinase]]
+[[Category: Schwarzer N]]
-[[Category: Transferase]]