1ndc
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(New page: 200px<br /><applet load="1ndc" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ndc, resolution 2.0Å" /> '''X-RAY STRUCTURE OF NU...)
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Revision as of 20:02, 20 November 2007
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X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION
Overview
We report the crystal structure of nucleoside diphosphate kinase (NDP, kinase) from Dictyostelium discoideum with thymidine diphosphate (dTDP), and Mg2+ bound at the active site. The structure has been refined to an, R-factor of 18.3% at 2-A resolution. The base stacks on the aromatic ring, of Phe 64 near the protein surface and is wedged between the side chains, of Phe 64 and Val 116. The sugar and the pyrophosphate are deeper inside, the protein and make numerous H-bonds with protein side chains. There is, no backbone interaction with the nucleotide. A Mg2+ ion bridges the alpha-, and beta-phosphates and interacts with the protein via water molecules., NDP kinase shows little specificity toward ribonucleotides and, deoxyribonucleotides. This property, required by the enzyme biological, function, can now be analyzed by comparing the crystal structures of free, ADP-ligated, and dTDP-ligated enzymes. The most significant differences, are located in residues 60-64, which adapt their conformation to allow Phe, 64 to stack on both types of bases. Nonspecific binding is achieved by the, absence of polar interaction between the base and protein atoms. The, ribose of ADP and the deoxyribose of dTDP occupy similar positions, their, hydroxyl groups interacting with Lys 16 and Asn 119. The H-bond between, Lys 16 and the O2' hydroxyl of ADP is replaced by a similar interaction, with a water molecule in the dTDP complex. The beta-phosphate position is, the same for ADP and dTDP, suggesting that the mechanism of phosphate, transfer is the same for all substrates ofNDP kinase.(ABSTRACT TRUNCATED, AT 250 WORDS)
About this Structure
1NDC is a Single protein structure of sequence from Dictyostelium discoideum with MG and TYD as ligands. Active as Nucleoside-diphosphate kinase, with EC number 2.7.4.6 Full crystallographic information is available from OCA.
Reference
X-ray structure of nucleoside diphosphate kinase complexed with thymidine diphosphate and Mg2+ at 2-A resolution., Cherfils J, Morera S, Lascu I, Veron M, Janin J, Biochemistry. 1994 Aug 9;33(31):9062-9. PMID:8049207
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