Nucleoside diphosphate kinase: Difference between revisions

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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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'''Nucleoside diphosphate kinase''' (NDK) catalyzes the transfer of phosphate from nucleoside triphosphate to nucleoside diphosphate.  This reaction is a multi-step reaction and is  used for the synthesis of nucleoside triphosphates other than ATP.  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 polimerization.


==3D structures of nucleoside diphosphate kinase==
== Function ==
'''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.


[[1ndk]], [[1npk]], [[1s5z]] – DdNDK – ''Dictyostelium discoideum''<BR />
== Disease ==
[[1nlk]] - DdNDK with phosphohistidine intermediate<BR />
NDKB deficiency causes diabetes-like vascular pathology<ref>PMID:25900369</ref>.
[[1leo]], [[1ncl]], [[1hlw]], [[1hhq]], [[1pae]] - DdNDK (mutant) <BR />
[[2nck]] – MxNDK – ''Myxococcus xanthus''<BR />
[[1ndl]] – DmNDK – ''Drosophila melanogaster''<BR />
[[1nsq]] - DmNDK with phosphohistidine intermediate<BR />
[[1nsk]], [[1jxv]], [[3l7u]] - hNDK A – human<BR />
[[1ehw]] - hNDK 4 (mutant) <BR />
[[1k44]] – NDK – ''Mycobacterium tuberculosis''<BR />
[[1nb2]] - NDK - ''Virgibacillus halodenitrificans''<BR />
[[1xiq]] - NDK A – ''Plasmodium falciparum''<BR />
[[1w7w]] - NDK – pea<BR />
[[1u8w]] - AtNDK I –'' Arabidopsis thaliana''<BR />
[[1s57]] - AtNDK II<BR />
[[1pku]] - NDK I – rice<BR />
[[1wkj]] - TtNDK – ''Thermus thermophilus''<BR />
[[1xqi]] - NDK (mutant) – ''Pyrobaculum aerophilum''<BR />
[[2az1]] - HsNDK – ''Halobacterium salinarum''<BR />
[[2hur]] - NDK – ''Escherichia coli''<BR />
[[3b54]] - NDK – yeast<BR />
[[2vu5]] - NDK – ''Bacillus anthracis''<BR />
[[2zua]] - NDK – ''Haloarcula quadrata''<BR />
[[3mpd]] - NDK – ''Encephalitozoon cuniculi''<BR />
[[3pj9]] - NDK – ''Campylobacter jejuni''<BR />
[[3r9l]] - NDK – ''Giardia lamblia''<BR />
[[3ngr]], [[3ngs]] - LmNDK – ''Leishmania major''<BR />
[[3prv]] - NDK – ''Trypanosoma cruzi''<BR />
[[3q83]] - SaNDK – ''Staphylococcus aureus''<BR />
[[4di6]] - BbNDK – ''Borrelia burgdorferi''<BR />
[[3ztq]], [[3zto]], [[3ztp]], [[3ztr]], [[3zts]] - NDK – ''Aquifex aeolicus''<BR />
[[4dut]] - NDK – ''Burkholderia thailandensis''


'''NDK complex with adenine derivative'''
== Structural highlights ==


[[1ndp]], [[kdn]], [[2bef]] – DdNDK + ADP<BR />
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>.
[[1b4s]] - DdNDK (mutant) + ADP<BR />
[[1bux]], [[1hiy]] - DdNDK + ADP derivative<br />
[[1nlk]] - MxNDK + ADP<BR />
[[2hvd]] - hNDK + ADP<BR />
[[1ucn]], [[2hve]] - hNDK (mutant) + ADP<BR />
[[1zs6]] - hNDK 3 + ADP<BR />
[[2dxd]] - PhNDK + ATP analog – ''Pyrococcus horikoshii''<BR />
[[2dy9]], [[2dya]] - PhNDK + ADP<BR />
[[3ngt]] - LmNDK + AMP<BR />
[[3ngu]] - LmNDK + ADP<BR />
[[3q8u]], [[3q8y]] - SaNDK + ADP<BR />
[[4dz6]] - BbNDK + ADP<BR />


==3D structures of nucleoside diphosphate kinase==
[[Nucleoside diphosphate kinase 3D structures]]


'''NDK complex with thymidine derivative'''
</StructureSection>
 
[[1f3f]] - DdNDK (mutant) + TDP derivative + TTP derivative<br />
[[1lwx]] - DdNDK (mutant) + azido-TDP<BR />
[[1f6t]] - DdNDK + TDP derivative<br />
[[1mn7]] - DdNDK (mutant) + TTP derivative<br />
[[1ndc]] - DdNDK + TDP<BR />
[[3ddi]] - ApNDK (mutant) + TDP – ''Acanthamoeba polyphaga''<BR />
[[3em1]], [[3evw]], [[3fbc]], [[3fbf]], [[3g2x]], [[3evo]] - ApNDK (mutant) + TDP derivative<br />
 
'''NDK complex with cytosine derivative'''
 
[[1nhk]] - MxNDK + CMP<BR />
[[2az3]] - HsNDK + CDP<BR />
[[3ee3]] - ApNDK + CDP<BR />
[[3etm]], [[3gpa]], [[3fc9]] - ApNDK (mutant) + CDP<BR />
[[3evm]] - ApNDK (mutant) + CDP derivative<br />
[[3q89]] - SaNDK + CDP<BR />
 
'''NDK complex with guanine derivative'''
 
[[1nue]] , [[3bbf]] - hNDK + GDP<BR />
[[1s59]] - AtNDK + GDP derivative + GTP derivative<br />
[[3bbb]] - hNDK B + GMP derivative + AMP derivative<br />
[[1wkk]] - TtNDK + GDP<BR />
[[2dxe]] - PhNDK + GDP<BR />
[[2dxf]] - PhNDK + GTP analog<BR />
[[3gp9]] - ApNDK + GDP<BR />
[[3b6b]] - ApNDK + GDP derivative<br />
[[3fbe]], [[3dkd]], [[3ejm]] - ApNDK (mutant) + GDP<BR />
[[3emt]], [[3ena]] - ApNDK (mutant) + GDP derivative<br />
[[3q86]] - SaNDK + GTP
 
'''NDK complex with uridine derivative'''
 
[[1b99]] - DdNDK + UDP derivative<br />
[[3eic]] - ApNDK + UDP<BR />
[[3elh]] - ApNDK + UDP derivative<br />
[[3fbb]], [[3fcv]] - ApNDK (mutant) + UDP derivative<br />
[[3fcw]] - ApNDK (mutant) + UDP<BR />
[[3q8v]] - SaNDK + UDP<BR />


[[1mn9,]] [[3fkb]] - DdNDK (mutant) + antiviral drug
== References ==
<references/>
[[Category:Topic Page]]

Latest revision as of 13:34, 11 November 2019


Function

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[1]. 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

NDKB deficiency causes diabetes-like vascular pathology[2].

Structural highlights

The biological assembly of Human nucleoside diphosphate kinase is . The NDK-adenine structure shows the [3]. Water molecules are shown as red spheres. .

3D structures of nucleoside diphosphate kinase

Nucleoside diphosphate kinase 3D structures


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

ReferencesReferences

  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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