6a9t

From Proteopedia

(Difference between revisions)

Current revision

Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 58 residues deletion)

Structural highlights

6a9t is a 1 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.15Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6a9t"

@@ Line 1: / Line 1: @@
 ==Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 58 residues deletion)==
-<StructureSection load='6a9t' size='340' side='right' caption='[[6a9t]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
+<StructureSection load='6a9t' size='340' side='right'caption='[[6a9t]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6a9t]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6A9T OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6A9T FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6a9t]] 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=6A9T OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6A9T 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=JEF:O-(O-(2-AMINOPROPYL)-O-(2-METHOXYETHYL)POLYPROPYLENE+GLYCOL+500)'>JEF</scene>, <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]] 2.15&#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=JEF:O-(O-(2-AMINOPROPYL)-O-(2-METHOXYETHYL)POLYPROPYLENE+GLYCOL+500)'>JEF</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</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=6a9t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a9t OCA], [http://pdbe.org/6a9t PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6a9t RCSB], [http://www.ebi.ac.uk/pdbsum/6a9t PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6a9t 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=6a9t FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6a9t OCA], [https://pdbe.org/6a9t PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6a9t RCSB], [https://www.ebi.ac.uk/pdbsum/6a9t PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6a9t 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 ==
@@ Line 23: / Line 23: @@
 __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]]

6a9t

From Proteopedia

Current revision

Crystal structure of Icp55 from Saccharomyces cerevisiae (N-terminal 58 residues deletion)

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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