1npk
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(New page: 200px<br /><applet load="1npk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1npk, resolution 1.80Å" /> '''REFINED X-RAY STRUCT...)
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Revision as of 20:20, 20 November 2007
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REFINED X-RAY STRUCTURE OF DICTYOSTELIUM NUCLEOSIDE DIPHOSPHATE KINASE AT 1,8 ANGSTROMS RESOLUTION
Overview
The X-ray structure of the nucleoside diphosphate kinase (NDP kinase) from, Dictyostelium discoideum has been refined at 1.8 A resolution from a, hexagonal crystal form with a 17 kDa monomer in its asymmetric unit. The, atomic model was derived from the previously determined structure of a, point mutant of the protein. It contains 150 amino acid residues out of, 155, and 95 solvent molecules. The R-factor is 0.196 and the estimated, accuracy of the average atomic position, 0.25 A. The Dictyostelium, structure is described in detail and compared to those of Drosophila and, Myxococcus xanthus NDP kinases. The protein is a hexamer with D3 symmetry., Residues 8 to 138 of each subunit form a globular alpha/beta domain. The, four-stranded beta-sheet is antiparallel; its topology is different from, other phosphate transfer enzymes, and also from the HPr protein which, like NDP kinase, carries a phosphorylated histidine. The same topology is, nevertheless found in several other proteins that bind mononucleotides, RNA or DNA. Strand connections in NDP kinase involve alpha-helices and a, 20-residue segment called the Kpn loop. The beta-sheet is regular except, for a beta-bulge in edge strand beta 2 and a gamma-turn at residue Ile120, just preceding strand beta 4. The latter may induce strain in the main, chain near the active site His122. The alpha 1 beta 2 motif participates, in forming dimers within the hexamer, helices alpha 1 and alpha 3, the Kpn, loop and C terminus, in forming trimers. The subunit fold and dimer, interactions found in Dictyostelium are conserved in other NDP kinases., Trimer interactions probably occur in all eukaryotic enzymes. They are, absent in the bacterial Myxococcus xanthus enzyme which is a tetramer, even though the subunit structure is very similar. In Dictyostelium, contacts between Kpn loops near the 3-fold axis block access to a central, cavity lined with polar residues and filled with well-defined solvent, molecules. Biochemical data on point mutants highlight the contribution of, the Kpn loop to protein stability. In Myxococcus, the Kpn loops are on the, tetramer surface and their sequence is poorly conserved. Yet, their, conformation is maintained and they make a similar contribution to the, substrate binding site.
About this Structure
1NPK is a Single protein structure of sequence from Dictyostelium discoideum. Active as Nucleoside-diphosphate kinase, with EC number 2.7.4.6 Full crystallographic information is available from OCA.
Reference
Refined X-ray structure of Dictyostelium discoideum nucleoside diphosphate kinase at 1.8 A resolution., Morera S, LeBras G, Lascu I, Lacombe ML, Veron M, Janin J, J Mol Biol. 1994 Nov 11;243(5):873-90. PMID:7966307
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