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1q33

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(New page: 200px<br /> <applet load="1q33" size="450" color="white" frame="true" align="right" spinBox="true" caption="1q33, resolution 1.81&Aring;" /> '''Crystal structure o...)
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[[Image:1q33.gif|left|200px]]<br />
 
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<applet load="1q33" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1q33, resolution 1.81&Aring;" />
 
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'''Crystal structure of human ADP-ribose pyrophosphatase NUDT9'''<br />
 
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==Overview==
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==Crystal structure of human ADP-ribose pyrophosphatase NUDT9==
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Human ADP-ribose pyrophosphatase NUDT9 belongs to a superfamily of Nudix, hydrolases that catabolize potentially toxic compounds in the cell. The, enzyme hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5'-phosphate. NUDT9, shares 39% sequence identity with the C-terminal cytoplasmic domain of the, ADPR-gated calcium channel TRPM2, which exhibits low but specific enzyme, activity. We determined crystal structures of NUDT9 in the presence and in, the absence of the reaction product ribose 5'-phosphate. On the basis of, these structures and comparison with a bacterial homologue, a model of the, substrate complex was built. The structure and activity of a double point, mutant (R(229)E(230)F(231) to R(229)I(230)L(231)), which mimics the Nudix, signature of the ion channel domain, was determined. Finally, the, activities of a pair of additional mutated constructs were compared to the, wild-type enzyme. The first corresponds to a minimal Nudix domain missing, an N-terminal domain and C-terminal tail; the second disrupts two, potential general bases in the active site. NUDT9 contains an N-terminal, domain with a novel fold and a catalytic C-terminal Nudix domain. Unlike, its closest functional homologue (homodimeric Escherichia coli ADPRase), it is active as a monomer, and the substrate is bound in a cleft between, the domains. The structure of the RIL mutant provides structural basis for, the reduced activity of the TRPM2 ion channel. The conformation and, binding interactions of ADPR substrate are predicted to differ from those, observed for E.coli ADPRase; mutation of structurally aligned acidic, residues in their active sites produce significantly different effects on, catalytic efficiency, indicating that their reaction pathways and, mechanisms may have diverged.
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<StructureSection load='1q33' size='340' side='right'caption='[[1q33]], [[Resolution|resolution]] 1.81&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1q33]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1Q33 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1Q33 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]] 1.81&#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=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1q33 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1q33 OCA], [https://pdbe.org/1q33 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1q33 RCSB], [https://www.ebi.ac.uk/pdbsum/1q33 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1q33 ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/NUDT9_HUMAN NUDT9_HUMAN] Hydrolyzes ADP-ribose (ADPR) to AMP and ribose 5'-phosphate.
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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/q3/1q33_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=1q33 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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1Q33 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] with GLC and SO4 as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/ADP-ribose_diphosphatase ADP-ribose diphosphatase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.6.1.13 3.6.1.13] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1Q33 OCA].
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*[[ADP-ribose pyrophosphatase 3D structures|ADP-ribose pyrophosphatase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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The crystal structure and mutational analysis of human NUDT9., Shen BW, Perraud AL, Scharenberg A, Stoddard BL, J Mol Biol. 2003 Sep 12;332(2):385-98. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12948489 12948489]
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[[Category: ADP-ribose diphosphatase]]
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[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Perraud, A.L.]]
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[[Category: Perraud AL]]
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[[Category: Scharenberg, A.]]
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[[Category: Scharenberg A]]
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[[Category: Shen, B.W.]]
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[[Category: Shen BW]]
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[[Category: Stoddard, B.L.]]
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[[Category: Stoddard BL]]
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[[Category: GLC]]
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[[Category: SO4]]
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[[Category: nudix fold]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 12 18:49:54 2007''
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Current revision

Crystal structure of human ADP-ribose pyrophosphatase NUDT9

PDB ID 1q33

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