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Nucleoside diphosphate kinase

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== Structural highlights ==
== Structural highlights ==
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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>.
+
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>.
 +
 
 +
==3D structures of nucleoside diphosphate kinase==
 +
[[Nucleoside diphosphate kinase 3D structures]]
 +
 
</StructureSection>
</StructureSection>
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*'''Nucleoside diphosphate kinase'''
*'''Nucleoside diphosphate kinase'''
 +
**[[1nsk]], [[1jxv]], [[3l7u]], [[4eno]] - hNDK A – human<BR />
 +
**[[1ehw]] - hNDK 4 (mutant) <BR />
 +
**[[3bbc]] - hNDK B (mutant)<br />
 +
**[[1vya]] – NDK – maize<br />
 +
**[[1w7w]] - NDK – pea<BR />
 +
**[[1pku]] - NDK I – rice<BR />
 +
**[[3b54]] - NDK – yeast<BR />
**[[1ndk]], [[1npk]], [[1s5z]] – DdNDK – ''Dictyostelium discoideum''<BR />
**[[1ndk]], [[1npk]], [[1s5z]] – DdNDK – ''Dictyostelium discoideum''<BR />
**[[1nlk]], [[1nsp]] - DdNDK with phosphohistidine intermediate<BR />
**[[1nlk]], [[1nsp]] - DdNDK with phosphohistidine intermediate<BR />
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**[[1ndl]], [[3wx8]] – DmNDK – ''Drosophila melanogaster''<BR />
**[[1ndl]], [[3wx8]] – DmNDK – ''Drosophila melanogaster''<BR />
**[[1nsq]] - DmNDK with phosphohistidine intermediate<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 />
**[[1k44]], [[4anc]] – MtNDK – ''Mycobacterium tuberculosis''<BR />
-
**[[4and]], [[4ane]] - MtNDK (mutant)<br />
+
**[[4and]], [[4ane]], [[6qa2]] - MtNDK (mutant)<br />
**[[1nb2]] - NDK - ''Virgibacillus halodenitrificans''<BR />
**[[1nb2]] - NDK - ''Virgibacillus halodenitrificans''<BR />
**[[1xiq]] - NDK A – ''Plasmodium falciparum''<BR />
**[[1xiq]] - NDK A – ''Plasmodium falciparum''<BR />
-
**[[1w7w]] - NDK – pea<BR />
 
**[[1u8w]] - AtNDK I –'' Arabidopsis thaliana''<BR />
**[[1u8w]] - AtNDK I –'' Arabidopsis thaliana''<BR />
**[[1s57]] - AtNDK II<BR />
**[[1s57]] - AtNDK II<BR />
-
**[[1pku]] - NDK I – rice<BR />
 
**[[1wkj]] - TtNDK – ''Thermus thermophilus''<BR />
**[[1wkj]] - TtNDK – ''Thermus thermophilus''<BR />
**[[1xqi]] - NDK (mutant) – ''Pyrobaculum aerophilum''<BR />
**[[1xqi]] - NDK (mutant) – ''Pyrobaculum aerophilum''<BR />
**[[2az1]] - HsNDK – ''Halobacterium salinarum''<BR />
**[[2az1]] - HsNDK – ''Halobacterium salinarum''<BR />
**[[2hur]] - NDK – ''Escherichia coli''<BR />
**[[2hur]] - NDK – ''Escherichia coli''<BR />
-
**[[3b54]] - NDK – yeast<BR />
+
 
**[[2vu5]] - NDK – ''Bacillus anthracis''<BR />
**[[2vu5]] - NDK – ''Bacillus anthracis''<BR />
**[[2zua]] - NDK – ''Haloarcula quadrata''<BR />
**[[2zua]] - NDK – ''Haloarcula quadrata''<BR />
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**[[3vvu]] - NDK – reconstructed bacterial ancestral<br />
**[[3vvu]] - NDK – reconstructed bacterial ancestral<br />
**[[4f36]] – TbNDK – ''Trypanosoma brucei''<br />
**[[4f36]] – TbNDK – ''Trypanosoma brucei''<br />
-
**[[1vya]] – NDK – maize<br />
 
**[[4s0m]], [[4w98]], [[4wbf]], [[5yih]], [[5yol]] – NDK – ''Acinetobacter baumannii''<br />
**[[4s0m]], [[4w98]], [[4wbf]], [[5yih]], [[5yol]] – NDK – ''Acinetobacter baumannii''<br />
**[[5iol]], [[5iom]] - SmNDK – ''Schisostoma mansoni''<br />
**[[5iol]], [[5iom]] - SmNDK – ''Schisostoma mansoni''<br />
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**[[5x00]] – NDK – ''Vibrio cholerae''<br />
**[[5x00]] – NDK – ''Vibrio cholerae''<br />
**[[6ay1]] – NDK – ''Helicobacter pylori''<br />
**[[6ay1]] – NDK – ''Helicobacter pylori''<br />
 +
**[[6aes]] – NDK – ''Pseudomonas aeruginosa''<br />
 +
**[[6agy]] – NDK – ''Aspergillus fumigatus''<br />
 +
**[[6k3h]] – NDK – ''Aspergillus flavus''<br />
*NDK complex with adenine derivative
*NDK complex with adenine derivative
 +
**[[2hvd]] - hNDK + ADP<BR />
 +
**[[1ucn]], [[2hve]] - hNDK (mutant) + ADP<BR />
 +
**[[1zs6]] - hNDK 3 + ADP<BR />
 +
**[[4uof]], [[4uoh]] - sNDK + ADP derivative – shrimp <br />
**[[1ndp]], [[1kdn]], [[2bef]] – DdNDK + ADP<BR />
**[[1ndp]], [[1kdn]], [[2bef]] – DdNDK + ADP<BR />
**[[1b4s]] - DdNDK (mutant) + ADP<BR />
**[[1b4s]] - DdNDK (mutant) + ADP<BR />
**[[1bux]], [[1hiy]] - DdNDK + ADP derivative<br />
**[[1bux]], [[1hiy]] - DdNDK + ADP derivative<br />
**[[1nlk]] - MxNDK + ADP<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 />
**[[2dxd]] - PhNDK + ATP analog <BR />
**[[2dy9]], [[2dya]] - PhNDK + ADP<BR />
**[[2dy9]], [[2dya]] - PhNDK + ADP<BR />
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**[[4ek2]] - BtNDK + AMP derivative<br />
**[[4ek2]] - BtNDK + AMP derivative<br />
**[[4hr2]] - BtNDK + ADP<br />
**[[4hr2]] - BtNDK + ADP<br />
-
**[[4uof]], [[4uoh]] - sNDK + ADP derivative – shrimp <br />
 
**[[5kk8]] - SmNDK + ADP<br />
**[[5kk8]] - SmNDK + ADP<br />
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*NDK complex with cytosine derivative
*NDK complex with cytosine derivative
 +
**[[4uog]] - sNDK + CDP derivative <br />
**[[1nhk]] - MxNDK + CMP<BR />
**[[1nhk]] - MxNDK + CMP<BR />
**[[2az3]] - HsNDK + CDP<BR />
**[[2az3]] - HsNDK + CDP<BR />
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**[[3q89]] - SaNDK + CDP<BR />
**[[3q89]] - SaNDK + CDP<BR />
**[[4fkx]] - TbNDK + CDP<br />
**[[4fkx]] - TbNDK + CDP<br />
-
**[[4uog]] - sNDK + CDP derivative <br />
 
*NDK complex with guanine derivative
*NDK complex with guanine derivative
**[[1nue]] , [[3bbf]] - hNDK + GDP<BR />
**[[1nue]] , [[3bbf]] - hNDK + GDP<BR />
-
**[[1s59]] - AtNDK + GDP derivative + GTP derivative<br />
 
**[[3bbb]] - hNDK B + GMP derivative + AMP derivative<br />
**[[3bbb]] - hNDK B + GMP derivative + AMP derivative<br />
**[[1wkk]] - TtNDK + GDP<BR />
**[[1wkk]] - TtNDK + GDP<BR />
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**[[3q86]] - SaNDK + GTP<br />
**[[3q86]] - SaNDK + GTP<br />
**[[4fky]] - TbNDK + GTP<br />
**[[4fky]] - TbNDK + GTP<br />
 +
**[[1s59]] - AtNDK + GDP derivative + GTP derivative<br />
*NDK complex with uridine derivative
*NDK complex with uridine derivative
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*NDK other complexes
*NDK other complexes
 +
**[[5ui4]] - hNDK + imidazole derivative<br />
**[[1mn9]], [[3fkb]] - DdNDK (mutant) + antiviral drug<br />
**[[1mn9]], [[3fkb]] - DdNDK (mutant) + antiviral drug<br />
**[[4cp5]] - DdNDK (mutant) + PMPAPP<br />
**[[4cp5]] - DdNDK (mutant) + PMPAPP<br />
-
**[[5ui4]] - hNDK + imidazole derivative<br />
+
 
}}
}}
== References ==
== References ==
<references/>
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

Revision as of 10:33, 11 November 2019

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

3D structures of nucleoside diphosphate kinase

Updated on 11-November-2019

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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