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| | ==Fully activated A. thaliana legumain isoform gamma in complex with Ac-YVAD-CMK== | | ==Fully activated A. thaliana legumain isoform gamma in complex with Ac-YVAD-CMK== |
| - | <StructureSection load='5obt' size='340' side='right' caption='[[5obt]], [[Resolution|resolution]] 1.50Å' scene=''> | + | <StructureSection load='5obt' size='340' side='right'caption='[[5obt]], [[Resolution|resolution]] 1.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5obt]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OBT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5OBT FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5obt]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana] and [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5OBT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5OBT FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=0QE:CHLOROMETHANE'>0QE</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=SNN:L-3-AMINOSUCCINIMIDE'>SNN</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]] 1.5Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">At4g32940, F26P21.60 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0QE:CHLOROMETHANE'>0QE</scene>, <scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=SNN:L-3-AMINOSUCCINIMIDE'>SNN</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Legumain Legumain], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.22.34 3.4.22.34] </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=5obt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5obt OCA], [https://pdbe.org/5obt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5obt RCSB], [https://www.ebi.ac.uk/pdbsum/5obt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5obt ProSAT]</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=5obt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5obt OCA], [http://pdbe.org/5obt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5obt RCSB], [http://www.ebi.ac.uk/pdbsum/5obt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5obt ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/VPEG_ARATH VPEG_ARATH]] Asparagine-specific endopeptidase involved in the processing of vacuolar seed protein precursors into the mature forms (PubMed:10417725). Probably involved in post-translational proteolysis of seed storage proteins in the protein storage vacuole of developing seeds (PubMed:14688293).<ref>PMID:10417725</ref> <ref>PMID:14688293</ref> | + | [https://www.uniprot.org/uniprot/VPEG_ARATH VPEG_ARATH] Asparagine-specific endopeptidase involved in the processing of vacuolar seed protein precursors into the mature forms (PubMed:10417725). Probably involved in post-translational proteolysis of seed storage proteins in the protein storage vacuole of developing seeds (PubMed:14688293).<ref>PMID:10417725</ref> <ref>PMID:14688293</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Legumain]] | + | [[Category: Large Structures]] |
| - | [[Category: Brandstetter, H]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Dall, E]] | + | [[Category: Brandstetter H]] |
| - | [[Category: Zauner, B F]] | + | [[Category: Dall E]] |
| - | [[Category: Asparaginyl endopeptidase]] | + | [[Category: Zauner BF]] |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Peptide cyclase]]
| + | |
| - | [[Category: Vacuolar processing enzyme]]
| + | |
| Structural highlights
Function
VPEG_ARATH Asparagine-specific endopeptidase involved in the processing of vacuolar seed protein precursors into the mature forms (PubMed:10417725). Probably involved in post-translational proteolysis of seed storage proteins in the protein storage vacuole of developing seeds (PubMed:14688293).[1] [2]
Publication Abstract from PubMed
Legumain is a dual-function protease peptide ligase whose activities are of great interest to researchers studying plant physiology and to biotechnological applications. However, the molecular mechanisms determining the specificities for proteolysis and ligation are unclear because structural information on the substrate recognition by a fully activated plant legumain is unavailable. Here, we present the X-ray structure of Arabidopsis thaliana legumain isoform gamma (AtLEGgamma) in complex with the covalent peptidic Ac-YVAD chloro methyl ketone (CMK) inhibitor targeting the catalytic cysteine. Mapping of the specificity pockets preceding the substrate cleavage site explained the known substrate preference. The comparison of inhibited and free AtLEGgamma structures disclosed a substrate-induced disorder-order transition with synergistic rearrangements in the substrate recognition sites. Docking and in vitro studies with an AtLEGgamma ligase substrate, sunflower trypsin inhibitor (SFTI), revealed a canonical, protease substrate-like binding to the active site binding pockets preceding and following the cleavage site. We found the interaction of the second residue after the scissile bond, P2'-S2', to be critical for deciding on proteolysis versus cyclization. cis-trans-Isomerization of the cyclic peptide product triggered its release from the AtLEGgamma active site and prevented inadvertent cleavage. The presented integrative mechanisms of proteolysis and ligation (transpeptidation) explain the interdependence of legumain and its preferred substrates and provide a rational framework for engineering optimized proteases, ligases, and substrates.
Structural analyses of Arabidopsis thaliana legumain gamma reveal the differential recognition and processing of proteolysis and ligation substrates.,Zauner FB, Elsasser B, Dall E, Cabrele C, Brandstetter H J Biol Chem. 2018 Apr 8. pii: M117.817031. doi: 10.1074/jbc.M117.817031. PMID:29628443[3]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kinoshita T, Yamada K, Hiraiwa N, Kondo M, Nishimura M, Hara-Nishimura I. Vacuolar processing enzyme is up-regulated in the lytic vacuoles of vegetative tissues during senescence and under various stressed conditions. Plant J. 1999 Jul;19(1):43-53. PMID:10417725
- ↑ Gruis D, Schulze J, Jung R. Storage protein accumulation in the absence of the vacuolar processing enzyme family of cysteine proteases. Plant Cell. 2004 Jan;16(1):270-90. doi: 10.1105/tpc.016378. Epub 2003 Dec 19. PMID:14688293 doi:http://dx.doi.org/10.1105/tpc.016378
- ↑ Zauner FB, Elsasser B, Dall E, Cabrele C, Brandstetter H. Structural analyses of Arabidopsis thaliana legumain gamma reveal the differential recognition and processing of proteolysis and ligation substrates. J Biol Chem. 2018 Apr 8. pii: M117.817031. doi: 10.1074/jbc.M117.817031. PMID:29628443 doi:http://dx.doi.org/10.1074/jbc.M117.817031
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