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5k60

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Crystal structure of N-terminal amidase with Gln-Val peptide

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 ==Crystal structure of N-terminal amidase with Gln-Val peptide==
-<StructureSection load='5k60' size='340' side='right' caption='[[5k60]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+<StructureSection load='5k60' size='340' side='right'caption='[[5k60]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5k60]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K60 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K60 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5k60]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_CEN.PK113-7D Saccharomyces cerevisiae CEN.PK113-7D]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K60 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K60 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.9&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k5u|5k5u]], [[5k5v|5k5v]], [[5k61|5k61]], [[5k62|5k62]], [[5k63|5k63]], [[5k66|5k66]], [[5b62|5b62]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLN:GLUTAMINE'>GLN</scene>, <scene name='pdbligand=VAL:VALINE'>VAL</scene></td></tr>
-<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=5k60 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k60 OCA], [http://pdbe.org/5k60 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k60 RCSB], [http://www.ebi.ac.uk/pdbsum/5k60 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k60 ProSAT]</span></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=5k60 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k60 OCA], [https://pdbe.org/5k60 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k60 RCSB], [https://www.ebi.ac.uk/pdbsum/5k60 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k60 ProSAT]</span></td></tr>
 </table>
-<div style="background-color:#fffaf0;">
+== Function ==
-== Publication Abstract from PubMed ==
+[https://www.uniprot.org/uniprot/N1P8Q8_YEASC N1P8Q8_YEASC]
-The first step of the hierarchically organized Arg/N-end rule pathway of protein degradation is deamidation of the N-terminal glutamine and asparagine residues of substrate proteins to glutamate and aspartate, respectively. These reactions are catalyzed by the N-terminal amidase (Nt-amidase) Nta1 in fungi such as Saccharomyces cerevisiae, and by the glutamine-specific Ntaq1 and asparagine-specific Ntan1 Nt-amidases in mammals. To investigate the dual specificity of yeast Nta1 (yNta1) and the importance of second-position residues in Asn/Gln-bearing N-terminal degradation signals (N-degrons), we determined crystal structures of yNta1 in the apo state and in complex with various N-degron peptides. Both an Asn-peptide and a Gln-peptide fit well into the hollow active site pocket of yNta1, with the catalytic triad located deeper inside the active site. Specific hydrogen bonds stabilize interactions between N-degron peptides and hydrophobic peripheral regions of the active site pocket. Key determinants for substrate recognition were identified and thereafter confirmed by using structure-based mutagenesis. We also measured affinities between yNta1 (wild-type and its mutants) and specific peptides, and determined KM and kcat for peptides of each type. Together, these results elucidate, in structural and mechanistic detail, specific deamidation mechanisms in the first step of the N-end rule pathway.
-Structural basis for dual specificity of yeast N-terminal amidase in the N-end rule pathway.,Kim MK, Oh SJ, Lee BG, Song HK Proc Natl Acad Sci U S A. 2016 Nov 1;113(44):12438-12443. Epub 2016 Oct 17. PMID:27791147<ref>PMID:27791147</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 5k60" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Kim, M K]]
+[[Category: Large Structures]]
-[[Category: Lee, B G]]
+[[Category: Saccharomyces cerevisiae CEN PK113-7D]]
-[[Category: Oh, S J]]
+[[Category: Kim MK]]
-[[Category: Song, H K]]
+[[Category: Lee B-G]]
-[[Category: Hydrolase]]
+[[Category: Oh S-J]]
-[[Category: N-end rule]]
+[[Category: Song HK]]
-[[Category: Nitrilase superfamily]]
-[[Category: Nta1]]

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Crystal structure of N-terminal amidase with Gln-Val peptide

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