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 2.0&Aring;" /> '''X-RAY STRUCTURE OF NU...)
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[[Image:1ndc.jpg|left|200px]]<br /><applet load="1ndc" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1ndc, resolution 2.0&Aring;" />
 
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'''X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION'''<br />
 
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==Overview==
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==X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION==
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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)
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<StructureSection load='1ndc' size='340' side='right'caption='[[1ndc]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1ndc]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NDC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NDC FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TYD:THYMIDINE-5-DIPHOSPHATE'>TYD</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ndc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ndc OCA], [https://pdbe.org/1ndc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ndc RCSB], [https://www.ebi.ac.uk/pdbsum/1ndc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ndc ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/nd/1ndc_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1ndc ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1NDC is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Dictyostelium_discoideum Dictyostelium discoideum] with MG and TYD as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Nucleoside-diphosphate_kinase Nucleoside-diphosphate kinase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.7.4.6 2.7.4.6] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NDC OCA].
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*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8049207 8049207]
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[[Category: Dictyostelium discoideum]]
[[Category: Dictyostelium discoideum]]
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[[Category: Nucleoside-diphosphate kinase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Cherfils J]]
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[[Category: Cherfils, J.]]
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[[Category: Janin J]]
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[[Category: Janin, J.]]
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[[Category: Morera S]]
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[[Category: Morera, S.]]
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[[Category: MG]]
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[[Category: TYD]]
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[[Category: phosphotransferase]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 22:09:34 2007''
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Current revision

X-RAY STRUCTURE OF NUCLEOSIDE DIPHOSPHATE KINASE COMPLEXED WITH DTDP AND MG2+ AT 2 A RESOLUTION

PDB ID 1ndc

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