1hr9: Difference between revisions
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< | ==Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide== | ||
<StructureSection load='1hr9' size='340' side='right'caption='[[1hr9]], [[Resolution|resolution]] 3.01Å' scene=''> | |||
You may | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1hr9]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] 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=1HR9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1HR9 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.01Å</td></tr> | |||
- | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EPE:4-(2-HYDROXYETHYL)-1-PIPERAZINE+ETHANESULFONIC+ACID'>EPE</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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=1hr9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1hr9 OCA], [https://pdbe.org/1hr9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1hr9 RCSB], [https://www.ebi.ac.uk/pdbsum/1hr9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1hr9 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/MPPA_YEAST MPPA_YEAST] Cleaves presequences (transit peptides) from mitochondrial protein precursors. The cleavage sites typically contain an arginine at position -2 (in the N-terminal portion) from the scissible peptide bond in addition to other distal basic residues, and an aromatic residue at position +1. | |||
== Evolutionary Conservation == | |||
[[Image:Consurf_key_small.gif|200px|right]] | |||
Check<jmol> | |||
<jmolCheckbox> | |||
<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/hr/1hr9_consurf.spt"</scriptWhenChecked> | |||
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | |||
<text>to colour the structure by Evolutionary Conservation</text> | |||
</jmolCheckbox> | |||
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1hr9 ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
BACKGROUND: Mitochondrial processing peptidase (MPP) is a metalloendopeptidase that cleaves the N-terminal signal sequences of nuclear-encoded proteins targeted for transport from the cytosol to the mitochondria. Mitochondrial signal sequences vary in length and sequence, but each is cleaved at a single specific site by MPP. The cleavage sites typically contain an arginine at position -2 (in the N-terminal portion) from the scissile peptide bond in addition to other distal basic residues, and an aromatic residue at position +1. Mitochondrial import machinery recognizes amphiphilic helical conformations in signal sequences. However, it is unclear how MPP specifically recognizes diverse presequence substrates. RESULTS: The crystal structures of recombinant yeast MPP and a cleavage-deficient mutant of MPP complexed with synthetic signal peptides have been determined. MPP is a heterodimer; its alpha and beta subunits are homologous to the core II and core I proteins, respectively, of the ubiquinol-cytochrome c oxidoreductase complex. Crystal structures of two different synthetic substrate peptides cocrystallized with the mutant MPP each show the peptide bound in an extended conformation at the active site. Recognition sites for the arginine at position -2 and the +1 aromatic residue are observed. CONCLUSIONS: MPP bound two mitochondrial import presequence peptides in extended conformations in a large polar cavity. The presequence conformations differ from the amphiphilic helical conformation recognized by mitochondrial import components. Our findings suggest that the presequences adopt context-dependent conformations through mitochondrial import and processing, helical for recognition by mitochondrial import machinery and extended for cleavage by the main processing component. | |||
Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences.,Taylor AB, Smith BS, Kitada S, Kojima K, Miyaura H, Otwinowski Z, Ito A, Deisenhofer J Structure. 2001 Jul 3;9(7):615-25. PMID:11470436<ref>PMID:11470436</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 1hr9" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
== | [[Category: Large Structures]] | ||
== | |||
[[Category: | |||
[[Category: Saccharomyces cerevisiae]] | [[Category: Saccharomyces cerevisiae]] | ||
[[Category: Deisenhofer | [[Category: Saccharomyces cerevisiae S288C]] | ||
[[Category: Ito | [[Category: Deisenhofer J]] | ||
[[Category: Kitada | [[Category: Ito A]] | ||
[[Category: Kojima | [[Category: Kitada S]] | ||
[[Category: Miyaura | [[Category: Kojima K]] | ||
[[Category: Otwinowski | [[Category: Miyaura H]] | ||
[[Category: Smith | [[Category: Otwinowski Z]] | ||
[[Category: Taylor | [[Category: Smith BS]] | ||
[[Category: Taylor AB]] | |||
Latest revision as of 09:15, 9 August 2023
Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal PeptideYeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Malate Dehydrogenase Signal Peptide
Structural highlights
FunctionMPPA_YEAST Cleaves presequences (transit peptides) from mitochondrial protein precursors. The cleavage sites typically contain an arginine at position -2 (in the N-terminal portion) from the scissible peptide bond in addition to other distal basic residues, and an aromatic residue at position +1. Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedBACKGROUND: Mitochondrial processing peptidase (MPP) is a metalloendopeptidase that cleaves the N-terminal signal sequences of nuclear-encoded proteins targeted for transport from the cytosol to the mitochondria. Mitochondrial signal sequences vary in length and sequence, but each is cleaved at a single specific site by MPP. The cleavage sites typically contain an arginine at position -2 (in the N-terminal portion) from the scissile peptide bond in addition to other distal basic residues, and an aromatic residue at position +1. Mitochondrial import machinery recognizes amphiphilic helical conformations in signal sequences. However, it is unclear how MPP specifically recognizes diverse presequence substrates. RESULTS: The crystal structures of recombinant yeast MPP and a cleavage-deficient mutant of MPP complexed with synthetic signal peptides have been determined. MPP is a heterodimer; its alpha and beta subunits are homologous to the core II and core I proteins, respectively, of the ubiquinol-cytochrome c oxidoreductase complex. Crystal structures of two different synthetic substrate peptides cocrystallized with the mutant MPP each show the peptide bound in an extended conformation at the active site. Recognition sites for the arginine at position -2 and the +1 aromatic residue are observed. CONCLUSIONS: MPP bound two mitochondrial import presequence peptides in extended conformations in a large polar cavity. The presequence conformations differ from the amphiphilic helical conformation recognized by mitochondrial import components. Our findings suggest that the presequences adopt context-dependent conformations through mitochondrial import and processing, helical for recognition by mitochondrial import machinery and extended for cleavage by the main processing component. Crystal structures of mitochondrial processing peptidase reveal the mode for specific cleavage of import signal sequences.,Taylor AB, Smith BS, Kitada S, Kojima K, Miyaura H, Otwinowski Z, Ito A, Deisenhofer J Structure. 2001 Jul 3;9(7):615-25. PMID:11470436[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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