1bux: Difference between revisions

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New page: left|200px<br /><applet load="1bux" size="450" color="white" frame="true" align="right" spinBox="true" caption="1bux, resolution 2.8Å" /> '''3'-PHOSPHORYLATED NUC...
 
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[[Image:1bux.gif|left|200px]]<br /><applet load="1bux" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1bux, resolution 2.8&Aring;" />
'''3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE'''<br />


==Overview==
==3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE==
Nucleoside diphosphate (NDP) kinase catalyzes the phosphorylation of ribo-, and deoxyribonucleosides diphosphates into triphosphates. NDP kinase is, also involved in malignant tumors and was shown to activate in vitro, transcription of the c-myc oncogene by binding to its NHE sequence. The, structure of the complex of NDP kinase with bound ADP shows that the, nucleotide adopts a different conformation from that observed in other, phosphokinases with an internal H bond between the 3'-OH and the beta-O, made free by the phosphate transfer. We use intrinsic protein fluorescence, to investigate the inhibitory and binding potential of nucleotide, analogues phosphorylated in 3'-OH position of the ribose to both wild type, and F64W mutant NDP kinase from Dictyostelium discoideum. Due to their, 3'-phosphate, 5'-phosphoadenosine 3'-phosphate (PAP) and adenosine, 3'-phosphate 5'-phosphosulfate (PAPS) can be regarded as structural, analogues of enzyme-bound ADP. The KD of PAPS (10 microM) is three times, lower than the KD of ADP. PAPS also acts as a competitive inhibitor toward, natural substrates during catalysis, with a KI in agreement with binding, data. The crystal structure of the binary complex between Dictyostelium, NDP kinase and PAPS was solved at 2.8-A resolution. It shows a new mode of, nucleotide binding at the active site with the 3'-phosphate of PAPS, located near the catalytic histidine, at the same position as the, gamma-phosphate in the transition state. The sulfate group is directed, toward the protein surface. PAPS will be useful for the design of high, affinity drugs targeted to NDP kinases.
<StructureSection load='1bux' size='340' side='right'caption='[[1bux]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1bux]] 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=1BUX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BUX FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.8&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PPS:3-PHOSPHATE-ADENOSINE-5-PHOSPHATE+SULFATE'>PPS</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1bux FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bux OCA], [https://pdbe.org/1bux PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bux RCSB], [https://www.ebi.ac.uk/pdbsum/1bux PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bux ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/NDKC_DICDI NDKC_DICDI]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bu/1bux_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</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=1bux ConSurf].
<div style="clear:both"></div>


==About this Structure==
==See Also==
1BUX 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 PPS as [http://en.wikipedia.org/wiki/ligand ligand]. 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=1BUX OCA].
*[[Nucleoside diphosphate kinase 3D structures|Nucleoside diphosphate kinase 3D structures]]
 
__TOC__
==Reference==
</StructureSection>
3'-Phosphorylated nucleotides are tight binding inhibitors of nucleoside diphosphate kinase activity., Schneider B, Xu YW, Janin J, Veron M, Deville-Bonne D, J Biol Chem. 1998 Oct 30;273(44):28773-8. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=9786875 9786875]
[[Category: Dictyostelium discoideum]]
[[Category: Dictyostelium discoideum]]
[[Category: Nucleoside-diphosphate kinase]]
[[Category: Large Structures]]
[[Category: Single protein]]
[[Category: Deville-Bonne D]]
[[Category: Deville-Bonne, D.]]
[[Category: Janin J]]
[[Category: Janin, J.]]
[[Category: Schneider B]]
[[Category: Schneider, B.]]
[[Category: Veron M]]
[[Category: Veron, M.]]
[[Category: Xu Y]]
[[Category: Xu, Y.]]
[[Category: PPS]]
[[Category: inhibitor]]
[[Category: paps]]
[[Category: phosphotransferase]]
 
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Latest revision as of 06:39, 7 February 2024

3'-PHOSPHORYLATED NUCLEOTIDES BINDING TO NUCLEOSIDE DIPHOSPHATE KINASE

1bux, resolution 2.80Å

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