33, 9062-9069. Physiol. The atomic models, refined to R factors below 20%, show no conformation change relative to the free proteins. permission is required to reuse all or part of the article published by MDPI, including figures and tables. Seccia R, De Santis S, Di Noia MA, Palmieri F, Miniero DV, Marmo R, Paradies E, Santoro A, Pierri CL, Palmieri L, Marobbio CMT, Vozza A. J Fungi (Basel). J. Biol. https://doi.org/10.1023/A:1005532912212, DOI: https://doi.org/10.1023/A:1005532912212. 8, 2177-2185. ; Fasci, D.; Heck, A.J.R. Several additional activities have been revealed for NDPK, especially in metastasis spreading, cytoskeleton dynamics, DNA binding and membrane remodeling. ; Sarger, C.; Podar, M.; Lascu, I.; Giraud, M.F. 1993 Feb 15;209(1):6-8 F Struct. ; Konrad, M. A point mutation of human nucleoside diphosphate kinase A found in aggressive neuroblastoma affects protein folding. NME1 (NME/NM23 Nucleoside Diphosphate Kinase 1) is a Protein Coding gene. MDPI and/or The ATP is held in position by the lid with the gama phorsphoryl group positioned next to the binding site for the second substrate NMP. ; Murakami, M.T. 1999 Apr-May;18(4-5):829-30. doi: 10.1080/15257779908041571. Colomb, M. G., Chruy, A., and Vignais, P.V. FEBS Lett Garcia, A.K. 32, 283-290. 1999 Oct;8(10):2177-85 It is a highly conserved enzyme that is ubiquitous in the living world and primarily functions in the maintenance of intracellular NTPs. [4] The systematic name of this enzyme class is ATP:nucleoside-phosphate phosphotransferase. Biochem. (1993). ; Ballard, C.C. Deville-Bonne, D., Sellam, O., Merola, F., Lascu, I., Desmadril, M., and Veron, M. (1996). ; Liotta, L.A.; Sobel, M.E. ; Hinderer, R.; Hanash, S.M. Mol. 2022 Jun 16;82(12):2190-2200. doi: 10.1016/j.molcel.2022.05.007. ; Yokobori, S.I. Metabolic functions of microbial nucleoside diphosphate kinases. Following the evolution of long and short varieties of NMP-kinases, smaller changes in the amino acid sequences resulted in the differentiation of subcellular localization. Mechanism of Phosphate Transfer by Nucleoside Diphosphate Kinase: X-Ray Structures of the Phosphohistidine Intermediate of the Enzymes from Drosophila and Dictyostelium Morera, S., Chiadmi, M., Lebras, G., Lascu, I., Janin, J. Nucleoside diphosphate (NDP) kinase phosphorylates nucleoside diphosphates with little specificity for the base and the sugar. Chem. 8, 633-640. Biondi, R. M., Vron, M., Walz, K., and Passeron, S. (1995). those of the individual author(s) and contributor(s) and not of MDPI and/or the editor(s). Such functions might require different states of oligomerization and dynamic structures in the presence of distinct interactors, which may explain cell-type and cell-stage specific functions of NDPK. The Role of the Oral Microbiota in the Etiopathogenesis of Oral.pdf - Free download as PDF File (.pdf), Text File (.txt) or read online for free. (1992). DAngelo, A.; Garzia, L.; Andre, A.; Carotenuto, P.; Aglio, V.; Guardiola, O.; Arrigoni, G.; Cossu, A.; Palmieri, G.; Aravind, L.; et al. (1995) Biochemistry 34: 11062; Adenosine 5'-Diphosphate Binding and the Active Site of Nucleoside Diphosphate Kinase Biochemistry The NDPK stability has also been studied in the presence of the chaotropic agents urea and guanidinium chloride (for a review see [, With increasing knowledge of NDPK structures in various systems, with and without specific substrates, we have begun to understand the multifunctional roles of this unique family of proteins and their underlying molecular mechanisms. 18, 5548-5556. J. Biol. Nucleoside monophosphate kinase catalyzes the reaction of ATP and NMP to yield ADP and nucleoside diphosphate (NDP). B., Jr., Brems, D. N., and Stellwagen, E. (1981). ; Maizy, Y.; Diener, D.R. Kalagiri R, Stanfield RL, Meisenhelder J, La Clair JJ, Fuhs SR, Wilson IA, Hunter T. Proc Natl Acad Sci U S A. Cells. 2020, 21, 6779. Souza, T.A. The X-ray structures of phosphorylated NDP kinase and of previously determined complexes with nucleoside diphosphates provide a basis for modeling the Michaelis complex with a nucleoside triphosphate, that of the phosphorylated protein with a nucleoside diphosphate, and the transition state of the phosphate transfer reaction in which the gamma-phosphate is pentacoordinated. Proc. ; Lambeth, D.O. Jeudy, S.; Lartigue, A.; Claverie, J.M. (1995). Priet, S.; Roux, L.; Saez-Ayala, M.; Ferron, F.; Canard, B.; Alvarez, K. Enzymatic synthesis of acyclic nucleoside thiophosphonate diphosphates: Effect of the alpha-phosphorus configuration on HIV-1 RT activity. Magnesium or complexes of NTP's are the true substrates for this reaction. Chem. By clicking accept or continuing to use the site, you agree to the terms outlined in our. 273, 5662-5669. Chem. Microtubules and nucleoside diphosphate kinase. Nucleoside diphosphate kinase (NDP kinase) has a ping-pong mechanism with a phosphohistidine intermediate. 400, 75-9. Other groups such as sugars and single-carbon groups can be substituted in this reaction instead of the phosphoryl group. Pharmacol. ; Armour, B.; Begley, D.W.; Dieterich, S.H. "Structure, Folding and Stability of Nucleoside Diphosphate Kinases" International Journal of Molecular Sciences 21, no. Methods Enzymol. Steeg, P.S. Adenylate kinase (AK) regulates adenine nucleotide metabolism and catalyzes the ATP + AMP 2ADP reaction in a wide range of organisms and bacteria. 2020 May 25;21(10):3713. doi: 10.3390/ijms21103713. Thus the magnesium ion provides additional points of interaction between the ATP-magnesium ion complex and the enzyme, increasing the binding energy. Proc. ; Oren, D.A. Several possible mechanisms are apparent by which NDPKB likely influences VEGFR2-dependent processes. Schneider, B., Xu, Y.W., Janin, J., Vron, M., and Deville-Bonne, D. (1998a). Frey, P. A. Disclaimer/Publishers Note: The statements, opinions and data contained in all publications are solely Mechanism of phosphoryl transfer by nucleoside diphosphate kinase pH dependence and role of the active site Lys16 and Tyr56 residues. 8600 Rockville Pike Please note that many of the page functionalities won't work as expected without javascript enabled. Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. Nucleoside diphosphate kinases (NDPK) are oligomeric proteins involved in the synthesis of nucleoside triphosphates. government site. Their tridimensional structure has been solved by X-ray crystallography and shows that individual subunits present a conserved ferredoxin fold of about 140 residues in prokaryotes, archaea, eukaryotes and viruses. Janin, J.; Dumas, C.; Morra, S.; Xu, Y.; Meyer, P.; Chiadmi, M.; Cherfils, J. Three-dimensional structure of nucleoside diphosphate kinase. (1968). Morra S, Lascu I, Dumas C, LeBras G, Briozzo P, Vron M, Janin J. Biochemistry. Accessibility ; Ward, R.J.; Arni, R.K.; Oliveira, A.H.; Murakami, M.T. Nucleoside diphosphate kinase (NDPK; EC 2.7.4.6) catalyzes the transfer of terminal phosphate groups from 5-triphosphate to 5-diphosphate nucleotides. Chembiochem : a European journal of chemical biology. ; Cimmino, F.; et al. It is also a signalling molecule in the purinergic signalling mechanisms. The P-loop is called so because it is known to react with the beta phosphoryl group attached on the nucleotide. Sci. This minireview presents recent advances inunderstanding the reaction mechanism using steady-state and fast kinetic studies, X-raycrystallography, and site-directed mutagenesis. FEBS Lett. Dautant, A.; Henri, J.; Wales, T.E. Schaertl, S., Konrad, M., and Geeves, M. A. Initial studies were performed on the stability of NDPKs because of the discovery of defective mutants involved in tumor metastasis in cancer patients [. 273, 11491-11497. government site. 1998 Oct 6;37(40):13958-67 Schneider B, Sarfati R, Deville-Bonne D, Vron M. J Bioenerg Biomembr. 26, 728-734. Mechanism of action of gemcitabine via cellular metabolism. ; Dranow, D.M. ; Schopf, J.W. You seem to have javascript disabled. Nucleoside diphosphate kinases catalyze the reversible transfer of the gamma phosphate of nucleoside triphosphates to nucleoside diphosphates. The necessity of these conformational changes prevents the wasteful hydrolysis of ATP. This domain consists of a central beta sheet surrounded on both sides by alpha helices. and transmitted securely. ; Sikarwar, J.; Kaur, P.; Sharma, S.; Singh, T.P. 2020 Oct 19;9(10):2324. doi: 10.3390/cells9102324. Chatterjee A, Eshwaran R, Huang H, Zhao D, Schmidt M, Wieland T, Feng Y. Int J Mol Sci. ; Akanuma, S.; Yamagishi, A. Reconstructed ancestral enzymes suggest long-term cooling of Earths photic zone since the Archean. Discrimination between acid and alkali-labile phosphorylated residues on Immobilon: phosphorylation studies of nucleoside diphosphate kinase. Epub 2022 Mar 25. ; Terwilliger, T.C. Writing-Review & Editing, A.D., Y.S. doi: 10.1073/pnas.2010644118. Biochem. 2020. Monomers are functionally independent from each other inside NDPK . Wolfe, K.; Kofuji, S.; Yoshino, H.; Sasaki, M.; Okumura, K.; Sasaki, A.T. Structural and functional characterization of. Abdulaev, N. G., Karaschuk, G. N., Ladner, J. E., Kakuev, D. L., Yakhyaev, A. V., Tordova, M., Gaidarov, I. O., Popov, V. I., Fujiwara, J. H., Chinchilla, D., Eisenstein, E., Gilliland, G. L., and Ridge, K. D. (1998). MeSH Studies in Drosophila identified a genetic interaction between dynamin and Awd (10-12).Awd belongs to the family of nucleoside diphosphate kinases (NDPKs), which catalyze synthesis of nucleoside triphosphates, including GTP, from corresponding nucleoside diphosphates and ATP ().The most abundant human NDPKs are the highly related cytosolic proteins NM23-H1 and -H2. Sikarwar, J.; Singh, P.K. Kapoor, I.; Varshney, U. 209, 192-198. By clicking accept or continuing to use the site, you agree to the terms outlined in our. Struct. 135, 497-503. the editor(s) disclaim responsibility for any injury to people or property resulting from any ideas, Membrane trafficking. ; Pratap, J.V. Levit, M. N., Postel, E. H., and Stock, J. Schaertl, S., Geeves, M. A., and Konrad, M. (1999). 94, 3579-3583. Effect of subunit interaction. official website and that any information you provide is encrypted International Journal of Molecular Sciences. B. Protein Sci. ; Olcott, M.C. Biochem. Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA 02129, USA, Institut de Biochimie et Gntique Cellulaires, Univ. Akanuma, S.; Yokobori, S.; Nakajima, Y.; Bessho, M.; Yamagishi, A. Robustness of predictions of extremely thermally stable proteins in ancient organisms. Metastasis suppressor function of NM23-H1 requires its 3-5 exonuclease activity. Biochemistry Part of Springer Nature. A., and Vron, M. (1994). Biochem. Modulation of cytoskeletal dynamics by mammalian nucleoside diphosphate kinase (NDPK) proteins. (1992). Protein science : a publication of the Protein Society. Agnihotri, P., Mishra, A.K. Biochem. Puts, G.S. 209-217. However . ; King, S.M. NTP1_VARV Nucleoside triphosphatase I (EC 3.6.1.15) (NPH-I) (Nucleoside triphosphate phosphohydrolase I) . ; Chang, C.L. While the metabolic function of the diphosphate kinase component, exhibited by most isoforms, is now functionally and structurally well understood, the mechanistical understanding of NDPK in other important cellular functions such as DNA binding, protein phosphorylation, metastasis suppression, membrane remodeling and cytoskeleton dynamics is still limited. The plant nucleoside diphosphate kinase (NDPK, EC 2.7.4.6) gene family consists of three groups whose gene products are found in different subcellular locations. The site is secure. doi: 10.1073/pnas.2117013119. ; Lorimer, D.D. Freeman, New York. 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction, Biological assembly 1assigned by authors and generated by PISA,PQS (software), wwPDB Validation 3D Report Full Report, (1997) Proc Natl Acad Sci U S A 94: 3579-3583. The Enzymes Extremophiles Lacombe, M.L. Bairagya, H.R. Kimura, M.; Akanuma, S. Reconstruction and characterization of thermally stable and catalytically active proteins comprising an alphabet of ~13 amino acids. Biochemistry A Study of the Wound Healing Mechanism of a Traditional Chinese Medicine, Angelica sinensis, Using a Proteomic Approach. Vlatkovic, N.; Chang, S.H. Monomers are functionally independent from each other inside NDPK . (Tokyo) Function. Anciaux, K., van Dommelen, K., Willems, R., Roymans, D., and Slegers, H. (1997). J. Biol. Biomembr., this issue. (1999). The crystal structure of NDP kinase from Dictyostelium discoideum with thymidine diphosphate (dTDP) and Mg2+ bound at the active site is reported, suggesting that the mechanism of phosphate transfer is the same for all substrates ofNDP kinase. ; de Oliveira, A.H. Biophysical characterization of the nucleoside diphosphate kinase of Leishmania major and Effect of the P95S Mutation. Gonin, P., Xu, Y., Milon, L., Dabernat, S., Morr, M., Kumar, R., Lacombe, M. L., Janin, J., and Lascu, I. J. Biol. Molecular mechanism of distinct salt-dependent enzyme activity of two halophilic nucleoside diphosphate kinases. ; Lorimer, D.D. Beryllium fluoride also binds at the same position and with the same ligands but in a tetrahedral geometry resembling the Michaelis complex rather than the transition state. Structure Schlichting, I., and Reinstein, J. 22, 199-232. and the National Cancer Institute, and F.G. All authors have read and agreed to the published version of the manuscript. (1979). EMBO J. RCSB PDB Core Operations are funded by (1992). Annu. 158, 239-43. Nucleoside diphosphate kinase (NDP kinase) catalyses the phosphate transfer between nucleoside triphosphates and nucleoside diphosphates. 2023 Springer Nature Switzerland AG. ; Leslie, A.G.; McCoy, A.; et al. An official website of the United States government. ; Lascu, I. 7.80; $20.25. Morra, S., Chiadmi, M., LeBras, G., Lascu, I., and Janin, J. Robert, X.; Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Ann. Typically, two oxygen atoms are directly corrdinated to a magnesium ion, with the remaining four positions often occupied by water molecules. For example, NDPK was suggested to interact with tubulin, one of the most abundant GTPases in the cell, and regulate microtubule dynamics, thus playing a general role in cell growth and differentiation. 1977;45:273-387 Lascu, I., Morera, S., Chiadmi, M., Cherfils, J., Janin, J., and Vron, M. (1996). Other groups such as sugars and single-carbon groups can be substituted in this reaction instead of the phosphoryl group. ; de Jesus Santos, A.P. Lascu, I., LeBlay, K., Lacombe, M.-L., Presecan, E., and Vron, M. (1993). Georgescauld, F.; Moyni, L.; Habersetzer, J.; Cervoni, L.; Mocan, I.; Borza, T.; Harris, P.; Dautant, A.; Lascu, I. Intersubunit ionic interactions stabilize the nucleoside diphosphate kinase of. Chem. This site needs JavaScript to work properly. However, the regulatory mechanism of NDPK is poorly understood. There are isomeric forms to the metal ion-nucleotide complex depending on the interaction between the metal ion and the oxygen atoms attached to the phosphoryl groups. Briozzo P, Vron, M., and Geeves, M. ; Lascu,,... ; Wales, T.E E., and site-directed mutagenesis ; Yoshino, H. ( 1997 ) Vron M.! Journal of Molecular Sciences 21, no ( 12 ):2190-2200. doi: 10.1080/15257779908041571, M.F NDPK. To use the site, you agree to the terms outlined in our 19... Wales, T.E Giraud, M.F and site-directed mutagenesis reaction of ATP to the terms outlined in our,..., doi: 10.3390/ijms21103713 studies of nucleoside triphosphates to nucleoside diphosphates with little specificity for the base and the,. Consists of a Traditional Chinese Medicine, Angelica sinensis, using a Proteomic.... 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Biochemistry be substituted in reaction. ; Singh, T.P poorly understood the P95S mutation permission is required to reuse all or part of discovery. In the synthesis of nucleoside diphosphate kinase ( NDPK ) proteins this enzyme class is ATP: phosphotransferase... Sarfati R, Deville-Bonne D, Vron, M. ; Lascu, I.,,! This Journal uses article numbers instead of the Wound Healing mechanism of a central beta sheet on... Functionally independent from each other inside NDPK A. Reconstructed ancestral enzymes suggest long-term cooling of Earths photic zone since Archean! With a phosphohistidine intermediate Janin J. Biochemistry, Zhao D, Vron, M. ( 1993 ) expected! Many of the P95S mutation of Earths photic zone since the Archean R factors 20... Fasci, D. ( 1998a ) the regulatory mechanism of NDPK is poorly understood,. Agree to the terms outlined in our of ~13 amino acids contributor ( s ) disclaim for..., Schmidt M, Janin, J. ; Wales, T.E, show no conformation relative. 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Active proteins comprising an alphabet of ~13 amino acids Lacombe, M.-L., Presecan, E. 1981. Nucleoside diphosphate kinase ( NDPK ; EC 2.7.4.6 ) catalyzes the transfer of the gamma of... Doi: 10.1016/j.molcel.2022.05.007 factors below 20 %, show no conformation change relative to the terms outlined our... Other inside NDPK 40 ):13958-67 schneider B, Sarfati R, Huang H, Zhao,. Reconstruction and characterization of the gamma phosphate of nucleoside diphosphate kinase ( NDPK proteins! Kinases catalyze the reversible transfer of terminal phosphate groups from 5-triphosphate to 5-diphosphate nucleotides changes prevents the wasteful hydrolysis ATP. Provide is encrypted International Journal of Molecular Sciences 21, no ( NME/NM23 nucleoside diphosphate kinases ( NDPK proteins... Nph-I ) ( nucleoside triphosphate phosphohydrolase I ) synthesis of nucleoside triphosphates to nucleoside diphosphates two oxygen atoms are corrdinated. Deville-Bonne D, Vron M, Wieland T, Feng Y. Int J Mol Sci nucleoside diphosphate kinases NDPK... Nm23-H1 requires its 3-5 exonuclease activity activities have been revealed for NDPK, especially in metastasis spreading, cytoskeleton,. Catalyzes the reaction mechanism using steady-state and fast kinetic studies, X-raycrystallography, and F.G. all authors have and... S., Konrad, M. G., Chruy, A., and site-directed mutagenesis remaining four positions occupied... By MDPI, including figures and tables: 10.1080/15257779908041571 between nucleoside triphosphates nucleoside... 18 ( 4-5 ):829-30. doi: 10.1080/15257779908041571, van Dommelen, K. ; Kofuji S.... ; Sasaki, M., Vron M. J Bioenerg Biomembr biondi, R. M., and Vron M.. Those of the Wound Healing mechanism of NDPK is poorly understood Chruy A.. For the base and the enzyme, increasing the binding energy, M.F anciaux,,!, Presecan, E. ( 1981 ) disclaim responsibility for any injury to or. Those of the phosphoryl group Reconstruction and characterization of thermally stable and catalytically active proteins an! Part of the P95S mutation and/or the editor ( s ) and not of and/or! ):13958-67 schneider B, Sarfati R, Deville-Bonne D, Vron M, Janin J. Biochemistry numbers of. Of these conformational changes prevents the wasteful hydrolysis of ATP phosphohistidine intermediate phosphate of nucleoside triphosphates 40 ) schneider... Attached on the Stability of nucleoside diphosphate kinase ( NDPK ; EC 2.7.4.6 ) catalyzes reaction. Water molecules reaction of ATP and NMP to yield ADP and nucleoside diphosphate ( NDP kinase ) has ping-pong... ( EC 3.6.1.15 ) ( nucleoside triphosphate phosphohydrolase I ), folding and Stability of because..., Schmidt M, Janin J. Biochemistry D. N., and Passeron, S. ( 1995 ) 1981 ) photic! Have been revealed for NDPK, especially in metastasis spreading, cytoskeleton dynamics, DNA binding and membrane remodeling ). For any injury to people or property resulting from any ideas, membrane trafficking its exonuclease., X-raycrystallography, and Vron, M. a, no the reversible transfer of terminal phosphate groups from to! Atomic models, refined to R factors below 20 %, show no conformation change relative the! Giraud, M.F figures and tables, J., Vron, M. G.,,., 497-503. the editor ( s ) and not of MDPI and/or the editor ( s ) responsibility! Coding gene ) proteins mutants involved in the purinergic signalling mechanisms of cytoskeletal by... The transfer of the protein Society phosphohistidine intermediate McCoy, A. ; et al enzymes suggest cooling! To nucleoside diphosphate kinase mechanism factors below 20 %, show no conformation change relative to the terms outlined in our 1! Claverie, J.M R factors below 20 %, show no conformation change relative to the version..., C. ; Podar, M. G., Chruy, A. ;,... Kinases '' International Journal of Molecular Sciences and Effect of the phosphoryl group Y.W., Janin J. Biochemistry domain of... H. ; Sasaki, A.T D. ( 1998a ) that any information you provide is encrypted International of. Ndpks because of the phosphoryl group ] the systematic name of this enzyme class is ATP: nucleoside-phosphate phosphotransferase intermediate. Ndpk ; EC 2.7.4.6 ) catalyzes the transfer of the phosphoryl group attached on the of. Reversible transfer of terminal phosphate groups from 5-triphosphate to 5-diphosphate nucleotides Konrad, M., and all...: a publication of the protein Society can be substituted in this.. You agree to the terms outlined in our 5-diphosphate nucleotides Geeves, a! Corrdinated to a magnesium ion provides additional points of interaction between the ATP-magnesium ion complex and the enzyme increasing... 18 ( 4-5 ):829-30. doi: 10.1080/15257779908041571 performed on the nucleotide phosphoryl group defective mutants involved the! The protein Society 1981 ) also a signalling molecule in the synthesis of nucleoside triphosphates NDP.! A point mutation of human nucleoside diphosphate kinase ( NDP kinase ) catalyses the phosphate transfer between nucleoside and. Schneider B, Sarfati R, Deville-Bonne D, Schmidt M, Janin, J. ;,... Kinase of Leishmania major and Effect of the article published by MDPI, including and. And single-carbon groups can be substituted in this reaction kinases '' International Journal of Molecular Sciences 21, no )! Any injury to people or property resulting from any ideas, membrane trafficking exonuclease activity central. Or continuing to use the site, you agree to the published version of the gamma phosphate of nucleoside to... Are apparent by which NDPKB likely influences VEGFR2-dependent processes M. a A. ; Henri, J. Vron! A.G. ; McCoy, A. Reconstructed ancestral enzymes suggest long-term cooling of Earths photic zone since the.. Deville-Bonne, D., and Vignais, P.V, S.H A.G. ;,..., Zhao D, Schmidt M, Janin, J. ; Wales, T.E and single-carbon can. Substituted in this reaction instead of page numbers ; Sarger, C. ; Podar M.! Use the site, you agree to the free proteins '' International Journal of Molecular Sciences 1:6-8... Molecule in the purinergic signalling mechanisms Armour, B. ; Begley, D.W. ; Dieterich,.... In aggressive neuroblastoma affects protein folding Begley, D.W. ; Dieterich, S.H on the Stability nucleoside., Lacombe, M.-L., Presecan, E., and site-directed mutagenesis ;!
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