1lwx

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[[Image:1lwx.jpg|left|200px]]<br /><applet load="1lwx" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1lwx, resolution 2.3&Aring;" />
 
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'''AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE'''<br />
 
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==Overview==
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==AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==
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To be effective as antiviral agent, AZT (3'-azido-3'-deoxythymidine) must be converted to a triphosphate derivative by cellular kinases. The conversion is inefficient and, to understand why AZT diphosphate is a poor substrate of nucleoside diphosphate (NDP) kinase, we determined a 2.3-A x-ray structure of a complex with the N119A point mutant of Dictyostelium NDP kinase. It shows that the analog binds at the same site and, except for the sugar ring pucker which is different, binds in the same way as the natural substrate thymidine diphosphate. However, the azido group that replaces the 3'OH of the deoxyribose in AZT displaces a lysine side chain involved in catalysis. Moreover, it is unable to make an internal hydrogen bond to the oxygen bridging the beta- and gamma-phosphate, which plays an important part in phosphate transfer.
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<StructureSection load='1lwx' size='340' side='right'caption='[[1lwx]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1lwx]] is a 3 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=1LWX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LWX 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]] 2.3&#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=AZD:3-AZIDO-3-DEOXYTHYMIDINE-5-DIPHOSPHATE'>AZD</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1lwx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1lwx OCA], [https://pdbe.org/1lwx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1lwx RCSB], [https://www.ebi.ac.uk/pdbsum/1lwx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1lwx 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/lw/1lwx_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=1lwx 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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1LWX 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 <scene name='pdbligand=MG:'>MG</scene> and <scene name='pdbligand=AZD:'>AZD</scene> 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1LWX 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 analysis of azido-thymidine diphosphate binding to nucleoside diphosphate kinase., Xu Y, Sellam O, Morera S, Sarfati S, Biondi R, Veron M, Janin J, Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7162-5. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9207061 9207061]
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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: Janin J]]
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[[Category: Janin, J.]]
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[[Category: Xu Y]]
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[[Category: Xu, Y.]]
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[[Category: AZD]]
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[[Category: MG]]
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[[Category: antiviral agent]]
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[[Category: azidothymidine]]
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[[Category: phosphotransferase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:49:22 2008''
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Current revision

AZT DIPHOSPHATE BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

PDB ID 1lwx

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