4hgd

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==Structural insights into yeast Nit2: C169S mutant of yeast Nit2 in complex with an endogenous peptide-like ligand==
==Structural insights into yeast Nit2: C169S mutant of yeast Nit2 in complex with an endogenous peptide-like ligand==
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<StructureSection load='4hgd' size='340' side='right' caption='[[4hgd]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
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<StructureSection load='4hgd' size='340' side='right'caption='[[4hgd]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[4hgd]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast] and [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HGD OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4HGD FirstGlance]. <br>
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<table><tr><td colspan='2'>[[4hgd]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4HGD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4HGD FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KGT:N-(4-CARBOXY-4-OXOBUTANOYL)-L-CYSTEINYLGLYCINE'>KGT</scene></td></tr>
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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]] 2.04&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4h5u|4h5u]], [[4hg3|4hg3]], [[4hg5|4hg5]]</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=CAC:CACODYLATE+ION'>CAC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=KGT:N-(4-CARBOXY-4-OXOBUTANOYL)-L-CYSTEINYLGLYCINE'>KGT</scene></td></tr>
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<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">J0706, NIT2, YJL126W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=4hgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hgd OCA], [https://pdbe.org/4hgd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4hgd RCSB], [https://www.ebi.ac.uk/pdbsum/4hgd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4hgd ProSAT]</span></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4hgd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4hgd OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4hgd RCSB], [http://www.ebi.ac.uk/pdbsum/4hgd PDBsum]</span></td></tr>
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</table>
</table>
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<div style="background-color:#fffaf0;">
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== Function ==
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== Publication Abstract from PubMed ==
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[https://www.uniprot.org/uniprot/NIT2_YEAST NIT2_YEAST]
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The Nit (nitrilase-like) protein subfamily constitutes branch 10 of the nitrilase superfamily. Nit proteins are widely distributed in nature. Mammals possess two members of the Nit subfamily, namely Nit1 and Nit2. Based on sequence similarity, yeast Nit2 (yNit2) is a homologue of mouse Nit1, a tumour-suppressor protein whose substrate specificity is not yet known. Previous studies have shown that mammalian Nit2 (also a putative tumour suppressor) is identical to omega-amidase, an enzyme that catalyzes the hydrolysis of alpha-ketoglutaramate (alpha-KGM) and alpha-ketosuccinamate (alpha-KSM) to alpha-ketoglutarate (alpha-KG) and oxaloacetate (OA), respectively. In the present study, crystal structures of wild-type (WT) yNit2 and of WT yNit2 in complex with alpha-KG and with OA were determined. In addition, the crystal structure of the C169S mutant of yNit2 (yNit2-C169S) in complex with an endogenous molecule of unknown structure was also solved. Analysis of the structures revealed that alpha-KG and OA are covalently bound to Cys169 by the formation of a thioester bond between the sulfhydryl group of the cysteine residue and the gamma-carboxyl group of alpha-KG or the beta-carboxyl group of OA, reflecting the presumed reaction intermediates. However, an enzymatic assay suggests that alpha-KGM is a relatively poor substrate of yNit2. Finally, a ligand was found in the active site of yNit2-C169S that may be a natural substrate of yNit2 or an endogenous regulator of enzyme activity. These crystallographic analyses provide information on the mode of substrate/ligand binding at the active site of yNit2 and insights into the catalytic mechanism. These findings suggest that yNit2 may have broad biological roles in yeast, especially in regard to nitrogen homeostasis, and provide a framework for the elucidation of the substrate specificity and biological role of mammalian Nit1.
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Structures of enzyme-intermediate complexes of yeast Nit2: insights into its catalytic mechanism and different substrate specificity compared with mammalian Nit2.,Liu H, Gao Y, Zhang M, Qiu X, Cooper AJ, Niu L, Teng M Acta Crystallogr D Biol Crystallogr. 2013 Aug;69(Pt 8):1470-81. doi:, 10.1107/S0907444913009347. Epub 2013 Jul 18. PMID:23897470<ref>PMID:23897470</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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== References ==
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<references/>
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__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Baker's yeast]]
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[[Category: Large Structures]]
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[[Category: Escherichia coli]]
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[[Category: Saccharomyces cerevisiae S288C]]
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[[Category: Gao, Y]]
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[[Category: Gao Y]]
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[[Category: Liu, H]]
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[[Category: Liu H]]
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[[Category: Niu, L]]
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[[Category: Niu L]]
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[[Category: Qiu, X]]
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[[Category: Qiu X]]
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[[Category: Teng, M]]
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[[Category: Teng M]]
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[[Category: Zhang, M]]
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[[Category: Zhang M]]
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[[Category: Hydrolase]]
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[[Category: Nitrilase superfamily]]
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[[Category: Omega-amidase]]
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Current revision

Structural insights into yeast Nit2: C169S mutant of yeast Nit2 in complex with an endogenous peptide-like ligand

PDB ID 4hgd

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