|
|
| Line 3: |
Line 3: |
| | <StructureSection load='6a9u' size='340' side='right'caption='[[6a9u]], [[Resolution|resolution]] 2.40Å' scene=''> | | <StructureSection load='6a9u' size='340' side='right'caption='[[6a9u]], [[Resolution|resolution]] 2.40Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6a9u]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A9U OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A9U FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6a9u]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Polypodiopsida Polypodiopsida] and [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=6A9U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A9U FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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]] 2.4Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=01B:(2S,3R)-3-AMINO-2-HYDROXY-4-PHENYLBUTANOIC+ACID'>01B</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=01B:(2S,3R)-3-AMINO-2-HYDROXY-4-PHENYLBUTANOIC+ACID'>01B</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ICP55, YER078C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=6a9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a9u OCA], [https://pdbe.org/6a9u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a9u RCSB], [https://www.ebi.ac.uk/pdbsum/6a9u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a9u ProSAT]</span></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='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=6a9u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a9u OCA], [http://pdbe.org/6a9u PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a9u RCSB], [http://www.ebi.ac.uk/pdbsum/6a9u PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a9u ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 25: |
Line 23: |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | |
| - | [[Category: Intermediate cleaving peptidase 55]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Goyal, V D]] | + | [[Category: Polypodiopsida]] |
| - | [[Category: Kumar, A]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Makde, R D]] | + | [[Category: Goyal VD]] |
| - | [[Category: Singh, R]] | + | [[Category: Kumar A]] |
| - | [[Category: Apstatin]] | + | [[Category: Makde RD]] |
| - | [[Category: Hydrolase]] | + | [[Category: Singh R]] |
| - | [[Category: Hydrolase-hydrolase inhibitor complex]]
| + | |
| - | [[Category: M24b]]
| + | |
| - | [[Category: Mitochondrial]]
| + | |
| - | [[Category: Peptidase]]
| + | |
| - | [[Category: Xaa-pro aminopeptidase]]
| + | |
| Structural highlights
Function
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.[1] [2]
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[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Naamati A, Regev-Rudzki N, Galperin S, Lill R, Pines O. Dual targeting of Nfs1 and discovery of its novel processing enzyme, Icp55. J Biol Chem. 2009 Oct 30;284(44):30200-8. Epub 2009 Aug 31. PMID:19720832 doi:http://dx.doi.org/M109.034694
- ↑ Vogtle FN, Wortelkamp S, Zahedi RP, Becker D, Leidhold C, Gevaert K, Kellermann J, Voos W, Sickmann A, Pfanner N, Meisinger C. Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell. 2009 Oct 16;139(2):428-39. PMID:19837041 doi:http://dx.doi.org/S0092-8674(09)01032-0
- ↑ Singh R, Goyal VD, Kumar A, Sabharwal NS, Makde RD. Crystal structures and biochemical analyses of intermediate cleavage peptidase: role of dynamics in enzymatic function. FEBS Lett. 2018 Dec 24. doi: 10.1002/1873-3468.13321. PMID:30582634 doi:http://dx.doi.org/10.1002/1873-3468.13321
|
