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| | ==E134A mutant nucleoside diphosphate kinase derived from Halomonas sp. 593== | | ==E134A mutant nucleoside diphosphate kinase derived from Halomonas sp. 593== |
| - | <StructureSection load='3vgu' size='340' side='right' caption='[[3vgu]], [[Resolution|resolution]] 2.30Å' scene=''> | + | <StructureSection load='3vgu' size='340' side='right'caption='[[3vgu]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vgu]] is a 8 chain structure with sequence from [http://en.wikipedia.org/wiki/Halomonas_sp._#593 Halomonas sp. #593]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VGU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VGU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3vgu]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Halomonas_sp._#593 Halomonas sp. #593]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VGU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VGU FirstGlance]. <br> |
| - | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[3vgs|3vgs]], [[3vgt|3vgt]], [[3vgv|3vgv]]</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]] 2.3Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">NDK ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=195704 Halomonas sp. #593])</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=3vgu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vgu OCA], [https://pdbe.org/3vgu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vgu RCSB], [https://www.ebi.ac.uk/pdbsum/3vgu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vgu 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=3vgu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vgu OCA], [http://pdbe.org/3vgu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vgu RCSB], [http://www.ebi.ac.uk/pdbsum/3vgu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vgu ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/Q83WH5_9GAMM Q83WH5_9GAMM]] 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.[HAMAP-Rule:MF_00451] | + | [https://www.uniprot.org/uniprot/Q83WH5_9GAMM Q83WH5_9GAMM] 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.[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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| | ==See Also== | | ==See Also== |
| - | *[[Nucleoside diphosphate kinase|Nucleoside diphosphate kinase]] | + | *[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Halomonas sp. #593]] | | [[Category: Halomonas sp. #593]] |
| - | [[Category: Nucleoside-diphosphate kinase]] | + | [[Category: Large Structures]] |
| - | [[Category: Arai, S]] | + | [[Category: Arai S]] |
| - | [[Category: Ishibashi, M]] | + | [[Category: Ishibashi M]] |
| - | [[Category: Kuroki, R]] | + | [[Category: Kuroki R]] |
| - | [[Category: Matsumoto, F]] | + | [[Category: Matsumoto F]] |
| - | [[Category: Okazaki, N]] | + | [[Category: Okazaki N]] |
| - | [[Category: Tamada, T]] | + | [[Category: Tamada T]] |
| - | [[Category: Tokunaga, H]] | + | [[Category: Tokunaga H]] |
| - | [[Category: Tokunaga, M]] | + | [[Category: Tokunaga M]] |
| - | [[Category: Yonezawa, Y]] | + | [[Category: Yonezawa Y]] |
| - | [[Category: Atp-binding]]
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| - | [[Category: Ferredoxin fold]]
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| - | [[Category: Halophilic]]
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| - | [[Category: Kinase]]
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| - | [[Category: Nucleotide-binding]]
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| - | [[Category: Transferase]]
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| Structural highlights
Function
Q83WH5_9GAMM 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.[HAMAP-Rule:MF_00451]
Publication Abstract from PubMed
Nucleoside diphosphate kinase (NDK) is known to form homotetramers or homohexamers. To clarify the oligomer state of NDK from moderately halophilic Halomonas sp. 593 (HaNDK), the oligomeric state of HaNDK was characterized by light scattering followed by X-ray crystallography. The molecular weight of HaNDK is 33,660, and the X-ray crystal structure determination to 2.3 and 2.7 A resolution showed a dimer form which was confirmed in the different space groups of R3 and C2 with an independent packing arrangement. This is the first structural evidence that HaNDK forms a dimeric assembly. Moreover, the inferred molecular mass of a mutant HaNDK (E134A) indicated 62.1-65.3 kDa, and the oligomerization state was investigated by X-ray crystallography to 2.3 and 2.5 A resolution with space groups of P2(1) and C2. The assembly form of the E134A mutant HaNDK was identified as a Type I tetramer as found in Myxococcus NDK. The structural comparison between the wild-type and E134A mutant HaNDKs suggests that the change from dimer to tetramer is due to the removal of negative charge repulsion caused by the E134 in the wild-type HaNDK. The higher ordered association of proteins usually contributes to an increase in thermal stability and substrate affinity. The change in the assembly form by a minimum mutation may be an effective way for NDK to acquire molecular characteristics suited to various circumstances.
A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase.,Arai S, Yonezawa Y, Okazaki N, Matsumoto F, Tamada T, Tokunaga H, Ishibashi M, Blaber M, Tokunaga M, Kuroki R Protein Sci. 2012 Apr;21(4):498-510. doi: 10.1002/pro.2032. Epub 2012 Mar 9. PMID:22275000[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Arai S, Yonezawa Y, Okazaki N, Matsumoto F, Tamada T, Tokunaga H, Ishibashi M, Blaber M, Tokunaga M, Kuroki R. A structural mechanism for dimeric to tetrameric oligomer conversion in Halomonas sp. nucleoside diphosphate kinase. Protein Sci. 2012 Apr;21(4):498-510. doi: 10.1002/pro.2032. Epub 2012 Mar 9. PMID:22275000 doi:10.1002/pro.2032
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