2yvm

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[[Image:2yvm.jpg|left|200px]]
 
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==Crystal structure of NDX2 in complex with MG2+ from thermus thermophilus HB8==
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The line below this paragraph, containing "STRUCTURE_2yvm", creates the "Structure Box" on the page.
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<StructureSection load='2yvm' size='340' side='right'caption='[[2yvm]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2yvm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus_HB8 Thermus thermophilus HB8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2YVM FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 1.7&#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></td></tr>
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{{STRUCTURE_2yvm| PDB=2yvm | SCENE= }}
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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=2yvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2yvm OCA], [https://pdbe.org/2yvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2yvm RCSB], [https://www.ebi.ac.uk/pdbsum/2yvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2yvm ProSAT], [https://www.topsan.org/Proteins/RSGI/2yvm TOPSAN]</span></td></tr>
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</table>
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'''Crystal structure of NDX2 in complex with MG2+ from thermus thermophilus HB8'''
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== Function ==
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[https://www.uniprot.org/uniprot/Q5SJY9_THET8 Q5SJY9_THET8]
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== Evolutionary Conservation ==
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==Overview==
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[[Image:Consurf_key_small.gif|200px|right]]
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ADP-ribose (ADPR) is one of the main substrates of Nudix proteins. Among the eight Nudix proteins of Thermus thermophilus HB8, we previously determined the crystal structure of Ndx4, an ADPR pyrophosphatase (ADPRase). In this study we show that Ndx2 of T. thermophilus also preferentially hydrolyzes ADPR and flavin adenine dinucleotide and have determined its crystal structure. We have determined the structures of Ndx2 alone and in complex with Mg2+, with Mg2+ and AMP, and with Mg2+ and a nonhydrolyzable ADPR analogue. Although Ndx2 recognizes the AMP moiety in a manner similar to those for other ADPRases, it recognizes the terminal ribose in a distinct manner. The residues responsible for the recognition of the substrate in Ndx2 are not conserved among ADPRases. This may reflect the diversity in substrate specificity among ADPRases. Based on these results, we propose the classification of ADPRases into two types: ADPRase-I enzymes, which exhibit high specificity for ADPR; and ADPRase-II enzymes, which exhibit low specificity for ADPR. In the active site of the ternary complexes, three Mg2+ ions are coordinated to the side chains of conserved glutamate residues and water molecules. Substitution of Glu90 and Glu94 with glutamine suggests that these residues are essential for catalysis. These results suggest that ADPRase-I and ADPRase-II enzymes have nearly identical catalytic mechanisms but different mechanisms of substrate recognition.
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Check<jmol>
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<jmolCheckbox>
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==About this Structure==
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/yv/2yvm_consurf.spt"</scriptWhenChecked>
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2YVM is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2YVM OCA].
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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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==Reference==
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</jmolCheckbox>
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Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8., Wakamatsu T, Nakagawa N, Kuramitsu S, Masui R, J Bacteriol. 2008 Feb;190(3):1108-17. Epub 2007 Nov 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18039767 18039767]
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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=2yvm ConSurf].
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[[Category: Single protein]]
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<div style="clear:both"></div>
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[[Category: Thermus thermophilus]]
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__TOC__
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[[Category: Kuramitsu, S.]]
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</StructureSection>
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[[Category: Masui, R.]]
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[[Category: Large Structures]]
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[[Category: Nakagawa, N.]]
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[[Category: Thermus thermophilus HB8]]
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[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
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[[Category: Kuramitsu S]]
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[[Category: Wakamatsu, T.]]
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[[Category: Masui R]]
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[[Category: Yokoyama, S.]]
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[[Category: Nakagawa N]]
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[[Category: Adp-ribose]]
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[[Category: Wakamatsu T]]
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[[Category: Fad]]
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[[Category: Yokoyama S]]
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[[Category: Hydrolase]]
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[[Category: National project on protein structural and functional analyse]]
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[[Category: Nppsfa]]
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[[Category: Nudix protein]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: Rsgi]]
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[[Category: Structural genomic]]
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[[Category: Thermus thermophilus]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 19:32:25 2008''
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Current revision

Crystal structure of NDX2 in complex with MG2+ from thermus thermophilus HB8

PDB ID 2yvm

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