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| | <StructureSection load='6qa2' size='340' side='right'caption='[[6qa2]], [[Resolution|resolution]] 2.20Å' scene=''> | | <StructureSection load='6qa2' size='340' side='right'caption='[[6qa2]], [[Resolution|resolution]] 2.20Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6qa2]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Mycta Mycta]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QA2 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6QA2 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6qa2]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Ra Mycobacterium tuberculosis H37Ra]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6QA2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6QA2 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</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]] 2.2Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ndk, MRA_2471 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=419947 MYCTA])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TAM:TRIS(HYDROXYETHYL)AMINOMETHANE'>TAM</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] </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=6qa2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qa2 OCA], [https://pdbe.org/6qa2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6qa2 RCSB], [https://www.ebi.ac.uk/pdbsum/6qa2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6qa2 ProSAT]</span></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=6qa2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6qa2 OCA], [http://pdbe.org/6qa2 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6qa2 RCSB], [http://www.ebi.ac.uk/pdbsum/6qa2 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6qa2 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NDK_MYCTA NDK_MYCTA]] Major role in the synthesis of nucleoside triphosphates other than ATP. The ATP gamma phosphate is transferred to the NDP beta phosphate via a ping-pong mechanism, using a phosphorylated active-site intermediate. | + | [https://www.uniprot.org/uniprot/NDK_MYCTU NDK_MYCTU] Major role in the synthesis of nucleoside triphosphates other than ATP.[HAMAP-Rule:MF_00451] |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6qa2" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6qa2" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Mycta]] | + | [[Category: Mycobacterium tuberculosis H37Ra]] |
| - | [[Category: Nucleoside-diphosphate kinase]]
| + | [[Category: Dautant A]] |
| - | [[Category: Dautant, A]] | + | [[Category: Engen JR]] |
| - | [[Category: Engen, J R]] | + | [[Category: Georgescauld F]] |
| - | [[Category: Georgescauld, F]] | + | [[Category: Henri J]] |
| - | [[Category: Henri, J]] | + | [[Category: Meyer P]] |
| - | [[Category: Meyer, P]] | + | [[Category: Wales TE]] |
| - | [[Category: Wales, T E]] | + | |
| - | [[Category: Open and closed binding site]]
| + | |
| - | [[Category: Remodeling]]
| + | |
| - | [[Category: Transferase]]
| + | |
| Structural highlights
Function
NDK_MYCTU Major role in the synthesis of nucleoside triphosphates other than ATP.[HAMAP-Rule:MF_00451]
Publication Abstract from PubMed
In order to be fully active and participate in the metabolism of phosphorylated nucleotides, most nucleoside diphosphate kinases (NDPK) have to assemble into stable hexamers. Here we studied the role played by six inter-subunit salt bridges R80-D93 in the stability of NDPK from the pathogen Mycobacterium tuberculosis ( Mt). Mutating R80 into Ala or Asn abolished the salt bridges. Unexpectedly, compensatory stabilizing mechanisms appeared for R80A and R80N mutants and we studied them by biochemical and structural methods. R80A mutant crystallized into I222 space group unusual for NDPK and its hexameric structure revealed occurrence at the trimer interface of a stabilizing hydrophobic patch around the mutation. Functionally relevant, a trimer of the R80A hexamer showed a remodeling of the binding site. In this conformation, the cleft of active site is more open, and then active His117 is more accessible to substrates. HDX-MS analysis of WT, R80A and R80N mutants showed that the remodeled region of the protein is highly solvent accessible indicating that equilibrium between open and closed conformation is possible. We propose that such equilibrium occurs in vivo and explains how bulky substrates access the catalytic His117.
Remodeling of the binding site of nucleoside diphosphate kinase revealed by X-Ray structure and H/D exchange.,Dautant A, Henri J, Wales TE, Meyer P, Engen JR, Georgescauld F Biochemistry. 2019 Feb 20. doi: 10.1021/acs.biochem.8b01308. PMID:30785730[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Dautant A, Henri J, Wales TE, Meyer P, Engen JR, Georgescauld F. Remodeling of the binding site of nucleoside diphosphate kinase revealed by X-Ray structure and H/D exchange. Biochemistry. 2019 Feb 20. doi: 10.1021/acs.biochem.8b01308. PMID:30785730 doi:http://dx.doi.org/10.1021/acs.biochem.8b01308
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