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6a9v

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Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 42 residues deletion)

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 ==Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 42 residues deletion)==
-<StructureSection load='6a9v' size='340' side='right' caption='[[6a9v]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
+<StructureSection load='6a9v' size='340' side='right'caption='[[6a9v]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6a9v]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A9V OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A9V FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6a9v]] is a 1 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=6A9V OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A9V FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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]] 2.9&#8491;</td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Intermediate_cleaving_peptidase_55 Intermediate cleaving peptidase 55], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.11.26 3.4.11.26] </span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GLY:GLYCINE'>GLY</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</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=6a9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a9v OCA], [http://pdbe.org/6a9v PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a9v RCSB], [http://www.ebi.ac.uk/pdbsum/6a9v PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a9v 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=6a9v FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a9v OCA], [https://pdbe.org/6a9v PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a9v RCSB], [https://www.ebi.ac.uk/pdbsum/6a9v PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a9v ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/ICP55_YEAST ICP55_YEAST]] Aminopeptidase which cleaves preprotein intermediates that carry destabilizing N-ter amino acid residues after the mitochondrial processing peptidase (MPP) cleavage site and is thus critical for stabilization of the mitochondrial proteome.<ref>PMID:19720832</ref> <ref>PMID:19837041</ref>
+[https://www.uniprot.org/uniprot/ICP55_YEAST ICP55_YEAST] Aminopeptidase which cleaves preprotein intermediates that carry destabilizing N-ter amino acid residues after the mitochondrial processing peptidase (MPP) cleavage site and is thus critical for stabilization of the mitochondrial proteome.<ref>PMID:19720832</ref> <ref>PMID:19837041</ref>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Intermediate cleavage peptidase (Icp55) processes a subset of mitochondrial matrix proteins by removing a bulky residue at their N termini, leaving behind smaller N-terminal residues (icp activity). This contributes towards the stability of the mitochondrial proteome. We report crystal structures of yeast Icp55 including one bound to the apstatin inhibitor. Apart from icp activity, the enzyme was found to exhibit Xaa-Pro aminopeptidase activity in vitro. Structural and biochemical data suggest that the enzyme exists in a rapid equilibrium between monomer and dimer. Furthermore, the dimer, and not the monomer, was found to be the active species with loop dynamics at the dimer interface playing an important role in activity. Based on the new evidence, we propose a model for binding and processing of cellular targets by Icp55. DATABASE: The atomic coordinates and structure factors for the structures of Icp55 (code 6A9T, 6A9U, 6A9V) have been deposited in the Protein Data Bank (PDB) (http://www.pdb.org/).
-Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function.,Singh R, Goyal VD, Kumar A, Sabharwal NS, Makde RD FEBS Lett. 2018 Dec 24. doi: 10.1002/1873-3468.13321. PMID:30582634<ref>PMID:30582634</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6a9v" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Intermediate cleaving peptidase 55]]
+[[Category: Large Structures]]
-[[Category: Goyal, V D]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Kumar, A]]
+[[Category: Goyal VD]]
-[[Category: Makde, R D]]
+[[Category: Kumar A]]
-[[Category: Singh, R]]
+[[Category: Makde RD]]
-[[Category: Hydrolase]]
+[[Category: Singh R]]
-[[Category: M24b]]
-[[Category: Mitochondrial]]
-[[Category: Peptidase]]
-[[Category: Xaa-pro aminopeptidase]]

6a9v

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Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 42 residues deletion)

Structural highlights

Function

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