5ld1: Difference between revisions
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==Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ATP== | |||
<StructureSection load='5ld1' size='340' side='right'caption='[[5ld1]], [[Resolution|resolution]] 2.09Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5ld1]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Meiothermus_ruber Meiothermus ruber]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5LD1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5LD1 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]] 2.09Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</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=5ld1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ld1 OCA], [https://pdbe.org/5ld1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ld1 RCSB], [https://www.ebi.ac.uk/pdbsum/5ld1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ld1 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®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 5ld1" style="background-color:#fffaf0;"></div> | ||
[[Category: | |||
[[Category: Kemper | ==See Also== | ||
[[Category: | *[[Phosphotransferase 3D structures|Phosphotransferase 3D structures]] | ||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Meiothermus ruber]] | |||
[[Category: Einsle O]] | |||
[[Category: Gerhardt S]] | |||
[[Category: Kemper F]] | |||
[[Category: Schwarzer N]] | |||
Latest revision as of 11:56, 11 October 2023
Crystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ATPCrystal Structure of Polyphosphate Kinase from Meiothermus ruber bound to ATP
Structural highlights
Publication Abstract from PubMedInorganic 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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