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| <StructureSection load='1ucn' size='450' 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'> | | <StructureSection load='1ucn' 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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| **[[4f36]] – TbNDK – ''Trypanosoma brucei''<br /> | | **[[4f36]] – TbNDK – ''Trypanosoma brucei''<br /> |
| **[[1vya]] – NDK – maize<br /> | | **[[1vya]] – NDK – maize<br /> |
| **[[4s0m]], [[4w98]], [[4wbf]] – 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 /> |
| **[[5u2i]] – NDK – ''Naegleria fowleri''<br /> | | **[[5u2i]] – NDK – ''Naegleria fowleri''<br /> |
| **[[5v6d]] – NDK – ''Neisseria gonnorrhoeae''<br /> | | **[[5v6d]] – NDK – ''Neisseria gonnorrhoeae''<br /> |
| | **[[5x00]] – NDK – ''Vibrio cholerae''<br /> |
| | **[[6ay1]] – NDK – ''Helicobacter pylori''<br /> |
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| *NDK complex with adenine derivative | | *NDK complex with adenine derivative |
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| **[[4f4a]] - TbNDK + UDP<br /> | | **[[4f4a]] - TbNDK + UDP<br /> |
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| *NDK complex with antiviral drug | | *NDK other complexes |
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| **[[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]] |
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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 homohexamer. The NDK-adenine structure shows the two reaction products: ADP and phosphate[3]. Ca coordination site. Water molecules shown as red spheres.
- ↑ 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
- ↑ 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:https://dx.doi.org/10.1007/s00592-015-0752-x
- ↑ 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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3D structures of nucleoside diphosphate kinase
Updated on 15-August-2018
{"openlevels":0}
- Nucleoside diphosphate kinase
- 1ndk, 1npk, 1s5z – DdNDK – Dictyostelium discoideum
- 1nlk, 1nsp - DdNDK with phosphohistidine intermediate
- 1leo, 1ncl, 1hlw, 1hhq, 1pae, 4c6a - DdNDK (mutant)
- 2nck – MxNDK – Myxococcus xanthus
- 1ndl, 3wx8 – DmNDK – Drosophila melanogaster
- 1nsq - DmNDK with phosphohistidine intermediate
- 1nsk, 1jxv, 3l7u, 4eno - hNDK A – human
- 1ehw - hNDK 4 (mutant)
- 3bbc - hNDK B (mutant)
- 1k44, 4anc – MtNDK – Mycobacterium tuberculosis
- 4and, 4ane - MtNDK (mutant)
- 1nb2 - NDK - Virgibacillus halodenitrificans
- 1xiq - NDK A – Plasmodium falciparum
- 1w7w - NDK – pea
- 1u8w - AtNDK I – Arabidopsis thaliana
- 1s57 - AtNDK II
- 1pku - NDK I – rice
- 1wkj - TtNDK – Thermus thermophilus
- 1xqi - NDK (mutant) – Pyrobaculum aerophilum
- 2az1 - HsNDK – Halobacterium salinarum
- 2hur - NDK – Escherichia coli
- 3b54 - NDK – yeast
- 2vu5 - NDK – Bacillus anthracis
- 2zua - NDK – Haloarcula quadrata
- 3mpd - NDK – Encephalitozoon cuniculi
- 3pj9 - NDK – Campylobacter jejuni
- 3r9l - NDK – Giardia lamblia
- 3ngr, 3ngs - LmNDK – Leishmania major
- 5c7p, 5caa, 5cab - LmNDK (mutant)
- 4kpc - NDK – Leishmania braziliensis
- 5go1 - NDK – Leishmania amazonensis
- 3prv - NDK – Trypanosoma cruzi
- 3q83 - SaNDK – Staphylococcus aureus
- 4di6 - BbNDK – Borrelia burgdorferi
- 3ztq, 3zto, 3ztp, 3ztr, 3zts - NDK – Aquifex aeolicus
- 4dut - BtNDK – Burkholderia thailandensis
- 2cwk - PhNDK – Pyrococcus horikoshii
- 3vgs, 3vgt - HaNDK – Halomonas
- 3vgu, 3vgv - HaNDK (mutant)
- 3vvt - NDK – reconstructed archaeal ancestral
- 3vvu - NDK – reconstructed bacterial ancestral
- 4f36 – TbNDK – Trypanosoma brucei
- 1vya – NDK – maize
- 4s0m, 4w98, 4wbf, 5yih, 5yol – NDK – Acinetobacter baumannii
- 5iol, 5iom - SmNDK – Schisostoma mansoni
- 5u2i – NDK – Naegleria fowleri
- 5v6d – NDK – Neisseria gonnorrhoeae
- 5x00 – NDK – Vibrio cholerae
- 6ay1 – NDK – Helicobacter pylori
- NDK complex with adenine derivative
- NDK complex with thymidine derivative
- 1f3f - DdNDK (mutant) + TDP derivative + TTP derivative
- 1lwx - DdNDK (mutant) + azido-TDP
- 1f6t - DdNDK + TDP derivative
- 1mn7 - DdNDK (mutant) + TTP derivative
- 1ndc - DdNDK + TDP
- 3ddi - ApNDK (mutant) + TDP – Acanthamoeba polyphaga
- 3em1, 3evw, 3fbc, 3fbf, 3g2x, 3evo - ApNDK (mutant) + TDP derivative
- NDK complex with cytosine derivative
- 1nhk - MxNDK + CMP
- 2az3 - HsNDK + CDP
- 3ee3 - ApNDK + CDP
- 3etm, 3gpa, 3fc9 - ApNDK (mutant) + CDP
- 3evm - ApNDK (mutant) + CDP derivative
- 3q89 - SaNDK + CDP
- 4fkx - TbNDK + CDP
- 4uog - sNDK + CDP derivative
- NDK complex with guanine derivative
- 1nue , 3bbf - hNDK + GDP
- 1s59 - AtNDK + GDP derivative + GTP derivative
- 3bbb - hNDK B + GMP derivative + AMP derivative
- 1wkk - TtNDK + GDP
- 2dxe - PhNDK + GDP
- 2dxf - PhNDK + GTP analog
- 3gp9 - ApNDK + GDP
- 3b6b - ApNDK + GDP derivative
- 3fbe, 3dkd, 3ejm - ApNDK (mutant) + GDP
- 3emt, 3ena - ApNDK (mutant) + GDP derivative
- 3q86 - SaNDK + GTP
4fky - TbNDK + GTP
- NDK complex with uridine derivative
- 1b99 - DdNDK + UDP derivative
- 3eic - ApNDK + UDP
- 3elh - ApNDK + UDP derivative
- 3fbb, 3fcv - ApNDK (mutant) + UDP derivative
- 3fcw - ApNDK (mutant) + UDP
- 3q8v - SaNDK + UDP
- 4f4a - TbNDK + UDP
- NDK other complexes
- 1mn9, 3fkb - DdNDK (mutant) + antiviral drug
- 4cp5 - DdNDK (mutant) + PMPAPP
- 5ui4 - hNDK + imidazole derivative
References
