Nucleoside diphosphate kinase

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{{STRUCTURE_1nsk| PDB=1nsk | SIZE=400| SCENE= |right|CAPTION=Human nucleoside diphosphate kinase hexamer, [[1nsk]] }}
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<StructureSection load='' size='350' side='right' caption='Human nucleoside diphosphate kinase complex with ADP, phosphate, TRIS and Ca+2 ion (green) (PDB entry [[1ucn]])' scene='48/487511/Cv/1'>
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== Function ==
== Function ==
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'''Nucleoside diphosphate kinase''' (NDK) catalyzes the exchange of phosphate between nucleoside triphosphate and nucleoside diphosphate. This reaction is a multi-step reaction which is used for the synthesis of nucleoside triphosphates other than ATP<ref>PMID:12972261</ref>. NDK provides nucleoside triphosphates for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerization.
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'''Nucleoside diphosphate kinase''' (NDK) catalyzes the exchange of phosphate between nucleoside triphosphate and nucleoside diphosphate. This reaction is a multi-step reaction which is used for the synthesis of nucleoside triphosphates other than ATP<ref>PMID:11768305</ref>. NDK provides nucleoside triphosphates for nucleic acid synthesis, CTP for lipid synthesis, UTP for polysaccharide synthesis and GTP for protein elongation, signal transduction and microtubule polymerization.
== Disease ==
== Disease ==
NDKB deficiency causes diabetes-like vascular pathology<ref>PMID:25900369</ref>.
NDKB deficiency causes diabetes-like vascular pathology<ref>PMID:25900369</ref>.
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==3D structures of nucleoside diphosphate kinase==
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== Structural highlights ==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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The biological assembly of Human nucleoside diphosphate kinase is <scene name='48/487511/Cv/7'>homohexamer</scene>. The NDK-adenine structure shows the <scene name='48/487511/Cv/8'>two reaction products: ADP and phosphate</scene><ref>PMID:12972261</ref>. Water molecules are shown as red spheres. <scene name='48/487511/Cv/9'>Ca coordination site</scene>.
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*'''Nucleoside diphosphate kinase'''
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==3D structures of nucleoside diphosphate kinase==
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[[Nucleoside diphosphate kinase 3D structures]]
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**[[1ndk]], [[1npk]], [[1s5z]] – DdNDK – ''Dictyostelium discoideum''<BR />
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**[[1nlk]], [[1nsp]] - DdNDK with phosphohistidine intermediate<BR />
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**[[1leo]], [[1ncl]], [[1hlw]], [[1hhq]], [[1pae]], [[4c6a]] - DdNDK (mutant) <BR />
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**[[2nck]] – MxNDK – ''Myxococcus xanthus''<BR />
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**[[1ndl]] – DmNDK – ''Drosophila melanogaster''<BR />
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**[[1nsq]] - DmNDK with phosphohistidine intermediate<BR />
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**[[1nsk]], [[1jxv]], [[3l7u]], [[4eno]] - hNDK A – human<BR />
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**[[1ehw]] - hNDK 4 (mutant) <BR />
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**[[3bbc]] - hNDK B (mutant)<br />
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**[[1k44]], [[4anc]] – MtNDK – ''Mycobacterium tuberculosis''<BR />
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**[[4and]], [[4ane]] - MtNDK (mutant)<br />
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**[[1nb2]] - NDK - ''Virgibacillus halodenitrificans''<BR />
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**[[1xiq]] - NDK A – ''Plasmodium falciparum''<BR />
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**[[1w7w]] - NDK – pea<BR />
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**[[1u8w]] - AtNDK I –'' Arabidopsis thaliana''<BR />
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**[[1s57]] - AtNDK II<BR />
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**[[1pku]] - NDK I – rice<BR />
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**[[1wkj]] - TtNDK – ''Thermus thermophilus''<BR />
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**[[1xqi]] - NDK (mutant) – ''Pyrobaculum aerophilum''<BR />
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**[[2az1]] - HsNDK – ''Halobacterium salinarum''<BR />
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**[[2hur]] - NDK – ''Escherichia coli''<BR />
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**[[3b54]] - NDK – yeast<BR />
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**[[2vu5]] - NDK – ''Bacillus anthracis''<BR />
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**[[2zua]] - NDK – ''Haloarcula quadrata''<BR />
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**[[3mpd]] - NDK – ''Encephalitozoon cuniculi''<BR />
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**[[3pj9]] - NDK – ''Campylobacter jejuni''<BR />
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**[[3r9l]] - NDK – ''Giardia lamblia''<BR />
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**[[3ngr]], [[3ngs]] - LmNDK – ''Leishmania major''<BR />
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**[[3prv]] - NDK – ''Trypanosoma cruzi''<BR />
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**[[3q83]] - SaNDK – ''Staphylococcus aureus''<BR />
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**[[4di6]] - BbNDK – ''Borrelia burgdorferi''<BR />
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**[[3ztq]], [[3zto]], [[3ztp]], [[3ztr]], [[3zts]] - NDK – ''Aquifex aeolicus''<BR />
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**[[4dut]] - BtNDK – ''Burkholderia thailandensis''<br />
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**[[2cwk]] - PhNDK – ''Pyrococcus horikoshii''<br />
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**[[3vgs]], [[3vgt]] - HaNDK – ''Halomonas''<br />
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**[[3vgu]], [[3vgv]] - HaNDK (mutant)<br />
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**[[3vvt]] - NDK – reconstructed archaeal ancestral<br />
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**[[3vvu]] - NDK – reconstructed bacterial ancestral<br />
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**[[4f36]] – TbNDK – ''Trypanosoma brucei''<br />
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*NDK complex with adenine derivative
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**[[1ndp]], [[1kdn]], [[2bef]] – DdNDK + ADP<BR />
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**[[1b4s]] - DdNDK (mutant) + ADP<BR />
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**[[1bux]], [[1hiy]] - DdNDK + ADP derivative<br />
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**[[1nlk]] - MxNDK + ADP<BR />
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**[[2hvd]] - hNDK + ADP<BR />
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**[[1ucn]], [[2hve]] - hNDK (mutant) + ADP<BR />
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**[[1zs6]] - hNDK 3 + ADP<BR />
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**[[2dxd]] - PhNDK + ATP analog <BR />
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**[[2dy9]], [[2dya]] - PhNDK + ADP<BR />
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**[[3ngt]] - LmNDK + AMP<BR />
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**[[3ngu]] - LmNDK + ADP<BR />
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**[[3q8u]], [[3q8y]] - SaNDK + ADP<BR />
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**[[4dz6]] - BbNDK + ADP<BR />
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**[[1wkl]] - TtNDK + ADP + ATP<br />
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**[[4ek2]] - BtNDK + AMP derivative<br />
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**[[4hr2]] - BtNDK + ADP<br />
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*NDK complex with thymidine derivative
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**[[1f3f]] - DdNDK (mutant) + TDP derivative + TTP derivative<br />
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**[[1lwx]] - DdNDK (mutant) + azido-TDP<BR />
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**[[1f6t]] - DdNDK + TDP derivative<br />
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**[[1mn7]] - DdNDK (mutant) + TTP derivative<br />
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**[[1ndc]] - DdNDK + TDP<BR />
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**[[3ddi]] - ApNDK (mutant) + TDP – ''Acanthamoeba polyphaga''<BR />
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**[[3em1]], [[3evw]], [[3fbc]], [[3fbf]], [[3g2x]], [[3evo]] - ApNDK (mutant) + TDP derivative<br />
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*NDK complex with cytosine derivative
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**[[1nhk]] - MxNDK + CMP<BR />
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**[[2az3]] - HsNDK + CDP<BR />
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**[[3ee3]] - ApNDK + CDP<BR />
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**[[3etm]], [[3gpa]], [[3fc9]] - ApNDK (mutant) + CDP<BR />
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**[[3evm]] - ApNDK (mutant) + CDP derivative<br />
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**[[3q89]] - SaNDK + CDP<BR />
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**[[4fkx]] - TbNDK + CDP<br />
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*NDK complex with guanine derivative
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**[[1nue]] , [[3bbf]] - hNDK + GDP<BR />
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**[[1s59]] - AtNDK + GDP derivative + GTP derivative<br />
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**[[3bbb]] - hNDK B + GMP derivative + AMP derivative<br />
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**[[1wkk]] - TtNDK + GDP<BR />
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**[[2dxe]] - PhNDK + GDP<BR />
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**[[2dxf]] - PhNDK + GTP analog<BR />
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**[[3gp9]] - ApNDK + GDP<BR />
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**[[3b6b]] - ApNDK + GDP derivative<br />
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**[[3fbe]], [[3dkd]], [[3ejm]] - ApNDK (mutant) + GDP<BR />
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**[[3emt]], [[3ena]] - ApNDK (mutant) + GDP derivative<br />
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**[[3q86]] - SaNDK + GTP
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*NDK complex with uridine derivative
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**[[1b99]] - DdNDK + UDP derivative<br />
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**[[3eic]] - ApNDK + UDP<BR />
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**[[3elh]] - ApNDK + UDP derivative<br />
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**[[3fbb]], [[3fcv]] - ApNDK (mutant) + UDP derivative<br />
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**[[3fcw]] - ApNDK (mutant) + UDP<BR />
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**[[3q8v]] - SaNDK + UDP<BR />
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**[[4f4a]] - TbNDK + UDP<br />
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*NDK complex with antiviral drug
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</StructureSection>
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**[[1mn9]], [[3fkb]] - DdNDK (mutant) + antiviral drug
 
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}}
 
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Current revision

Human nucleoside diphosphate kinase complex with ADP, phosphate, TRIS and Ca+2 ion (green) (PDB entry 1ucn)

Drag the structure with the mouse to rotate

References

  1. ↑ Janin J, Dumas C, Morera S, Xu Y, Meyer P, Chiadmi M, Cherfils J. Three-dimensional structure of nucleoside diphosphate kinase. J Bioenerg Biomembr. 2000 Jun;32(3):215-25. PMID:11768305
  2. ↑ Qiu Y, Zhao D, Butenschon VM, Bauer AT, Schneider SW, Skolnik EY, Hammes HP, Wieland T, Feng Y. Nucleoside diphosphate kinase B deficiency causes a diabetes-like vascular pathology via up-regulation of endothelial angiopoietin-2 in the retina. Acta Diabetol. 2016 Feb;53(1):81-9. doi: 10.1007/s00592-015-0752-x. Epub 2015 Apr, 23. PMID:25900369 doi:http://dx.doi.org/10.1007/s00592-015-0752-x
  3. ↑ Chen Y, Gallois-Montbrun S, Schneider B, Veron M, Morera S, Deville-Bonne D, Janin J. Nucleotide binding to nucleoside diphosphate kinases: X-ray structure of human NDPK-A in complex with ADP and comparison to protein kinases. J Mol Biol. 2003 Sep 26;332(4):915-26. PMID:12972261

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Michal Harel, Alexander Berchansky, Joel L. Sussman

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