Nucleoside diphosphate kinase: Difference between revisions

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{{STRUCTURE_1nsk| PDB=1nsk  | SIZE=400| SCENE= |right|CAPTION=Human nucleoside diphosphate kinase hexamer, [[1nsk]] }}
<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'>
 
== Function ==
== 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: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.
'''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>.  


==3D structures of nucleoside diphosphate kinase==
== Structural highlights ==
 
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
{{#tree:id=OrganizedByTopic|openlevels=0|


*'''Nucleoside diphosphate kinase'''
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>.


**[[1ndk]], [[1npk]], [[1s5z]] – DdNDK – ''Dictyostelium discoideum''<BR />
==3D structures of nucleoside diphosphate kinase==
**[[1nlk]], [[1nsp]] - DdNDK with phosphohistidine intermediate<BR />
[[Nucleoside diphosphate kinase 3D structures]]
**[[1leo]], [[1ncl]], [[1hlw]], [[1hhq]], [[1pae]], [[4c6a]] - DdNDK (mutant) <BR />
**[[2nck]] – MxNDK – ''Myxococcus xanthus''<BR />
**[[1ndl]] – DmNDK – ''Drosophila melanogaster''<BR />
**[[1nsq]] - DmNDK with phosphohistidine intermediate<BR />
**[[1nsk]], [[1jxv]], [[3l7u]], [[4eno]] - hNDK A – human<BR />
**[[1ehw]] - hNDK 4 (mutant) <BR />
**[[3bbc]] - hNDK B (mutant)<br />
**[[1k44]], [[4anc]] – MtNDK – ''Mycobacterium tuberculosis''<BR />
**[[4and]], [[4ane]] - MtNDK (mutant)<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]] - BtNDK – ''Burkholderia thailandensis''<br />
**[[2cwk]] - PhNDK – ''Pyrococcus horikoshii''<br />
**[[3vgs]], [[3vgt]] - HaNDK – ''Halomonas''<br />
**[[3vgu]], [[3vgv]] - HaNDK (mutant)<br />
**[[3vvt]] - NDK – reconstructed archaeal ancestral<br />
**[[3vvu]] - NDK – reconstructed bacterial ancestral<br />
**[[4f36]] – TbNDK – ''Trypanosoma brucei''<br />
 
*NDK complex with adenine derivative
 
**[[1ndp]], [[1kdn]], [[2bef]] – DdNDK + ADP<BR />
**[[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 <BR />
**[[2dy9]], [[2dya]] - PhNDK + ADP<BR />
**[[3ngt]] - LmNDK + AMP<BR />
**[[3ngu]] - LmNDK + ADP<BR />
**[[3q8u]], [[3q8y]] - SaNDK + ADP<BR />
**[[4dz6]] - BbNDK + ADP<BR />
**[[1wkl]] - TtNDK + ADP + ATP<br />
**[[4ek2]] - BtNDK + AMP derivative<br />
**[[4hr2]] - BtNDK + ADP<br />
 
*NDK complex with thymidine derivative
 
**[[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 />
**[[4fkx]] - TbNDK + 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 />
**[[4f4a]] - TbNDK + UDP<br />


*NDK complex with antiviral drug
</StructureSection>


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