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5xgx

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Current revision (10:18, 27 March 2024) (edit) (undo)
 
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<StructureSection load='5xgx' size='340' side='right'caption='[[5xgx]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
<StructureSection load='5xgx' size='340' side='right'caption='[[5xgx]], [[Resolution|resolution]] 2.33&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
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<table><tr><td colspan='2'>[[5xgx]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGX OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5XGX FirstGlance]. <br>
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<table><tr><td colspan='2'>[[5xgx]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Colwellia_psychrerythraea_34H Colwellia psychrerythraea 34H]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5XGX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XGX FirstGlance]. <br>
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</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DAS:D-ASPARTIC+ACID'>DAS</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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]] 2.33&#8491;</td></tr>
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<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5xgw|5xgw]]</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=DAS:D-ASPARTIC+ACID'>DAS</scene>, <scene name='pdbligand=DLY:D-LYSINE'>DLY</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5xgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgx OCA], [http://pdbe.org/5xgx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5xgx RCSB], [http://www.ebi.ac.uk/pdbsum/5xgx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgx ProSAT]</span></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=5xgx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xgx OCA], [https://pdbe.org/5xgx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xgx RCSB], [https://www.ebi.ac.uk/pdbsum/5xgx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xgx ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
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[[http://www.uniprot.org/uniprot/Q484B6_COLP3 Q484B6_COLP3]] Catalyzes the hydrolytic cleavage of a subset of L-isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins damaged by L-isoaspartyl residues formation.[PIRNR:PIRNR001238]
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[https://www.uniprot.org/uniprot/Q484B6_COLP3 Q484B6_COLP3] Catalyzes the hydrolytic cleavage of a subset of L-isoaspartyl (L-beta-aspartyl) dipeptides. Used to degrade proteins damaged by L-isoaspartyl residues formation.[PIRNR:PIRNR001238]
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Isoaspartyl dipeptidase (IadA) is an enzyme that catalyzes the hydrolysis of an isoaspartyl dipeptide-like moiety, which can be inappropriately formed in proteins, between the beta-carboxyl group side chain of Asp and the amino group of the following amino acid. Here, we have determined the structures of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea, both ligand-free and that complexed with beta-isoaspartyl lysine, at 1.85-A and 2.33-A resolution, respectively. In both structures, CpsIadA formed an octamer with two Zn ions in the active site. A structural comparison with Escherichia coli isoaspartyl dipeptidase (EcoIadA) revealed a major difference in the structure of the active site. For metal ion coordination, CpsIadA has a Glu166 residue in the active site, whereas EcoIadA has a post-translationally carbamylated-lysine 162 residue. Site-directed mutagenesis studies confirmed that the Glu166 residue is critical for CpsIadA enzymatic activity. This residue substitution from lysine to glutamate induces the protrusion of the beta12-alpha8 loop into the active site to compensate for the loss of length of the side chain. In addition, the alpha3-beta9 loop of CpsIadA adopts a different conformation compared to EcoIadA, which induces a change in the structure of the substrate-binding pocket. Despite CpsIadA having a different active-site residue composition and substrate-binding pocket, there is only a slight difference in CpsIadA substrate specificity compared with EcoIadA. Comparative sequence analysis classified IadA-containing bacteria and archaea into two groups based on the active-site residue composition, with Type I IadAs having a glutamate residue and Type II IadAs having a carbamylated-lysine residue. CpsIadA has maximal activity at pH 8-8.5 and 45 degrees C, and was completely inactivated at 60 degrees C. Despite being isolated from a psychrophilic bacteria, CpsIadA is thermostable probably owing to its octameric structure. This is the first conclusive description of the structure and properties of a Type I IadA.
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Crystal structure and functional characterization of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea strain 34H.,Park SH, Lee CW, Lee SG, Shin SC, Kim HJ, Park H, Lee JH PLoS One. 2017 Jul 19;12(7):e0181705. doi: 10.1371/journal.pone.0181705., eCollection 2017. PMID:28723955<ref>PMID:28723955</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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<div class="pdbe-citations 5xgx" style="background-color:#fffaf0;"></div>
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==See Also==
==See Also==
*[[Isoaspartyl dipeptidase|Isoaspartyl dipeptidase]]
*[[Isoaspartyl dipeptidase|Isoaspartyl dipeptidase]]
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== References ==
 
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<references/>
 
__TOC__
__TOC__
</StructureSection>
</StructureSection>
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[[Category: Colwellia psychrerythraea 34H]]
[[Category: Large Structures]]
[[Category: Large Structures]]
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[[Category: Lee, C W]]
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[[Category: Lee CW]]
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[[Category: Lee, J H]]
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[[Category: Lee JH]]
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[[Category: Park, S H]]
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[[Category: Park SH]]
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[[Category: Beta-isoaspartyl lysine]]
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[[Category: Colwellia psychrerythraea]]
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[[Category: Hydrolase]]
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[[Category: Iada]]
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[[Category: Isoaspartyl dipeptidase]]
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Current revision

Crystal structure of colwellia psychrerythraea strain 34H isoaspartyl dipeptidase E80Q mutant complexed with beta-isoaspartyl lysine

PDB ID 5xgx

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