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3ngs

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Current revision (10:00, 14 February 2024) (edit) (undo)
 
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<StructureSection load='3ngs' size='340' side='right'caption='[[3ngs]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
<StructureSection load='3ngs' size='340' side='right'caption='[[3ngs]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[3ngs]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Leima Leima]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NGS FirstGlance]. <br>
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<table><tr><td colspan='2'>[[3ngs]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Leishmania_major Leishmania major]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3NGS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3NGS FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3ngr|3ngr]], [[3ngt|3ngt]], [[3ngu|3ngu]]</div></td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DTT:2,3-DIHYDROXY-1,4-DITHIOBUTANE'>DTT</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">L1648.07, LmjF32.2950, NDKb ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=5664 LEIMA])</td></tr>
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<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ngs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ngs OCA], [https://pdbe.org/3ngs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ngs RCSB], [https://www.ebi.ac.uk/pdbsum/3ngs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ngs 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=3ngs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ngs OCA], [https://pdbe.org/3ngs PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ngs RCSB], [https://www.ebi.ac.uk/pdbsum/3ngs PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ngs ProSAT]</span></td></tr>
</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/Q9U1E1_LEIMA Q9U1E1_LEIMA]
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Nucleoside diphosphate kinases play a crucial role in the purine-salvage pathway of trypanosomatid protozoa and have been found in the secretome of Leishmania sp., suggesting a function related to host-cell integrity for the benefit of the parasite. Due to their importance for housekeeping functions in the parasite and by prolonging the life of host cells in infection, they become an attractive target for drug discovery and design. In this work, we describe the first structural characterization of nucleoside diphosphate kinases b from trypanosomatid parasites (tNDKbs) providing insights into their oligomerization, stability and structural determinants for nucleotide binding. Crystallographic studies of LmNDKb when complexed with phosphate, AMP and ADP showed that the crucial hydrogen-bonding residues involved in the nucleotide interaction are fully conserved in tNDKbs. Depending on the nature of the ligand, the nucleotide-binding pocket undergoes conformational changes, which leads to different cavity volumes. SAXS experiments showed that tNDKbs, like other eukaryotic NDKs, form a hexamer in solution and their oligomeric state does not rely on the presence of nucleotides or mimetics. Fluorescence-based thermal-shift assays demonstrated slightly higher stability of tNDKbs compared to human NDKb (HsNDKb), which is in agreement with the fact that tNDKbs are secreted and subjected to variations of temperature in the host cells during infection and disease development. Moreover, tNDKbs were stabilized upon nucleotide binding, whereas HsNDKb was not influenced. Contrasts on the surface electrostatic potential around the nucleotide-binding pocket might be a determinant for nucleotide affinity and protein stability differentiation. All these together demonstrated the molecular adaptation of parasite NDKbs in order to exert their biological functions intra-parasite and when secreted by regulating ATP levels of host cells.
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Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding.,Souza TA, Trindade DM, Tonoli CC, Santos CR, Ward RJ, Arni RK, Oliveira AH, Murakami MT Mol Biosyst. 2011 Apr 28. PMID:21528129<ref>PMID:21528129</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 3ngs" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Leima]]
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[[Category: Leishmania major]]
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[[Category: Nucleoside-diphosphate kinase]]
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[[Category: Arni RK]]
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[[Category: Arni, R K]]
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[[Category: Murakami MT]]
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[[Category: Murakami, M T]]
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[[Category: Oliveira AHC]]
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[[Category: Oliveira, A H.C]]
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[[Category: Santos CR]]
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[[Category: Santos, C R]]
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[[Category: Sousa TACB]]
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[[Category: Sousa, T A.C B]]
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[[Category: Tonoli CCC]]
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[[Category: Tonoli, C C.C]]
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[[Category: Trindade DM]]
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[[Category: Trindade, D M]]
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[[Category: Ward RJ]]
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[[Category: Ward, R J]]
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[[Category: Lmndkb]]
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[[Category: Ordered nucleotide-binding loop]]
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[[Category: Phosphate ion]]
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[[Category: Transferase]]
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Current revision

Structure of Leishmania nucleoside diphosphate kinase b with ordered nucleotide-binding loop

PDB ID 3ngs

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