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| | ==Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP== | | ==Crystal structure of the Mimivirus NDK N62L-R107G double mutant complexed with GDP== |
| - | <StructureSection load='3fbe' size='340' side='right' caption='[[3fbe]], [[Resolution|resolution]] 2.40Å' scene=''> | + | <StructureSection load='3fbe' size='340' side='right'caption='[[3fbe]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Apmv Apmv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3FBE FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3fbe]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Acanthamoeba_polyphaga_mimivirus Acanthamoeba polyphaga mimivirus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3FBE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3FBE FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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]] 2.4Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2b8p|2b8p]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">MIMI_R418, NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=212035 APMV])</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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [https://pdbe.org/3fbe PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [https://www.ebi.ac.uk/pdbsum/3fbe PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbe ProSAT]</span></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>
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| - | <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=3fbe FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3fbe OCA], [http://pdbe.org/3fbe PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3fbe RCSB], [http://www.ebi.ac.uk/pdbsum/3fbe PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3fbe ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/NDK_MIMIV NDK_MIMIV]] Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment. | + | [https://www.uniprot.org/uniprot/NDK_MIMIV NDK_MIMIV] Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment. |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | ==See Also== | | ==See Also== |
| - | *[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]] | + | *[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Apmv]] | + | [[Category: Acanthamoeba polyphaga mimivirus]] |
| - | [[Category: Nucleoside-diphosphate kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Abergel, C]] | + | [[Category: Abergel C]] |
| - | [[Category: Claverie, J M]] | + | [[Category: Claverie JM]] |
| - | [[Category: Jeudy, S]] | + | [[Category: Jeudy S]] |
| - | [[Category: Lartigue, A]] | + | [[Category: Lartigue A]] |
| - | [[Category: Atp-binding]]
| + | |
| - | [[Category: Kinase]]
| + | |
| - | [[Category: Magnesium]]
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| - | [[Category: Metal-binding]]
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| - | [[Category: Nucleotide metabolism]]
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| - | [[Category: Nucleotide-binding]]
| + | |
| - | [[Category: Phosphoprotein]]
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| - | [[Category: Phosphotransferase nucleotide binding]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
NDK_MIMIV Plays a role in the synthesis of nucleoside triphosphates. This activity may optimize the replication of the AT-rich (73%) viral genome in a thymidine-limited host environment.
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
The analysis of the Acanthamoeba polyphaga mimivirus genome revealed the first virus-encoded nucleoside diphosphate kinase (NDK), an enzyme that is central to the synthesis of RNA and DNA, ubiquitous in cellular organisms, and well conserved among the three domains of life. In contrast with the broad specificity of cellular NDKs for all types of ribo- and deoxyribonucleotides, the mimivirus enzyme exhibits a strongly preferential affinity for deoxypyrimidines. In order to elucidate the molecular basis of this unique substrate specificity, we determined the three-dimensional (3D) structure of the Acanthamoeba polyphaga mimivirus NDK alone and in complex with various nucleotides. As predicted from a sequence comparison with cellular NDKs, the 3D structure of the mimivirus enzyme exhibits a shorter Kpn loop, previously recognized as a main feature of the NDK active site. The structure of the viral enzyme in complex with various nucleotides also pinpointed two residue changes, both located near the active site and specific to the viral NDK, which could explain its stronger affinity for deoxynucleotides and pyrimidine nucleotides. The role of these residues was explored by building a set of viral NDK variants, assaying their enzymatic activities, and determining their 3D structures in complex with various nucleotides. A total of 26 crystallographic structures were determined at resolutions ranging from 2.8 A to 1.5 A. Our results suggest that the mimivirus enzyme progressively evolved from an ancestral NDK under the constraints of optimizing its efficiency for the replication of an AT-rich (73%) viral genome in a thymidine-limited host environment.
Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase.,Jeudy S, Lartigue A, Claverie JM, Abergel C J Virol. 2009 Jul;83(14):7142-50. Epub 2009 May 13. PMID:19439473[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Jeudy S, Lartigue A, Claverie JM, Abergel C. Dissecting the unique nucleotide specificity of mimivirus nucleoside diphosphate kinase. J Virol. 2009 Jul;83(14):7142-50. Epub 2009 May 13. PMID:19439473 doi:10.1128/JVI.00511-09
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