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| | ==Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L== | | ==Crystal Structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L== |
| - | <StructureSection load='3vta' size='340' side='right' caption='[[3vta]], [[Resolution|resolution]] 2.75Å' scene=''> | + | <StructureSection load='3vta' size='340' side='right'caption='[[3vta]], [[Resolution|resolution]] 2.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[3vta]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Cucumis_melo Cucumis melo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3VTA FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[3vta]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Cucumis_melo Cucumis melo]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3VTA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3VTA FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=DFP:DIISOPROPYL+PHOSPHONATE'>DFP</scene>, <scene name='pdbligand=FUC:ALPHA-L-FUCOSE'>FUC</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cucumisin Cucumisin], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.25 3.4.21.25] </span></td></tr> | + | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cucumisin Cucumisin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.21.25 3.4.21.25] </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=3vta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vta OCA], [http://pdbe.org/3vta PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3vta RCSB], [http://www.ebi.ac.uk/pdbsum/3vta PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3vta 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=3vta FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3vta OCA], [https://pdbe.org/3vta PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3vta RCSB], [https://www.ebi.ac.uk/pdbsum/3vta PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3vta ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | [[Category: Cucumis melo]] | | [[Category: Cucumis melo]] |
| | [[Category: Cucumisin]] | | [[Category: Cucumisin]] |
| | + | [[Category: Large Structures]] |
| | [[Category: Arima, K]] | | [[Category: Arima, K]] |
| | [[Category: Hosaka, T]] | | [[Category: Hosaka, T]] |
| Structural highlights
3vta is a 2 chain structure with sequence from Cucumis melo. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
| | Ligands: | , , , , |
| Activity: | Cucumisin, with EC number 3.4.21.25 |
| Resources: | FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT |
Publication Abstract from PubMed
Cucumisin is a plant serine protease, isolated as an extracellular glycoprotein from the melon fruit Cucumis melo L. var. Prince. Cucumisin is composed of multiple domain modules, including catalytic, protease-associated, and fibronectin-III-like domains. The crystal structure of cucumisin was determined by the multiwavelength anomalous dispersion method and refined at 2.75A resolution. A structural homology search indicated that the catalytic domain of cucumisin shares structural similarity with subtilisin and subtilisin-like fold enzymes. According to the Z-score, the highest structural similarity is with tomato subtilase 3 (SBT3), with an rmsd of 3.5A for the entire region. The dimer formation mediated by the protease-associated domain in SBT3 is a distinctive structural characteristic of cucumisin. On the other hand, analytical ultracentrifugation indicated that cucumisin is mainly monomeric in solution. Although the locations of the amino acid residues composing the catalytic triad are well conserved between cucumisin and SBT3, a disulfide bond is uniquely located near the active site of cucumisin. The steric circumstances of the active site with this disulfide bond are distinct from those of SBT3, and it contributes to the substrate preference of cucumisin, especially at the P2 position. Among the plant serine proteases, the thermostability of cucumisin is higher than that of its structural homologue SBT3, as determined by their melting points. A structural comparison between cucumisin and SBT3 revealed that cucumisin possesses less surface area and shortened loop regions. Consequently, the higher thermostability of cucumisin is achieved by its more compact structure.
Crystal structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L.,Murayama K, Kato-Murayama M, Hosaka T, Sotokawauchi A, Yokoyama S, Arima K, Shirouzu M J Mol Biol. 2012 Oct 26;423(3):386-96. doi: 10.1016/j.jmb.2012.07.013. Epub 2012 , Jul 24. PMID:22841692[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Murayama K, Kato-Murayama M, Hosaka T, Sotokawauchi A, Yokoyama S, Arima K, Shirouzu M. Crystal structure of cucumisin, a subtilisin-like endoprotease from Cucumis melo L. J Mol Biol. 2012 Oct 26;423(3):386-96. doi: 10.1016/j.jmb.2012.07.013. Epub 2012 , Jul 24. PMID:22841692 doi:10.1016/j.jmb.2012.07.013
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