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| | <StructureSection load='2deo' size='340' side='right'caption='[[2deo]], [[Resolution|resolution]] 3.00Å' scene=''> | | <StructureSection load='2deo' size='340' side='right'caption='[[2deo]], [[Resolution|resolution]] 3.00Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2deo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii Pyrococcus horikoshii]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEO FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2deo]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DEO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2DEO FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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]] 3Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">PH1510 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=70601 Pyrococcus horikoshii])</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</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=2deo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2deo OCA], [https://pdbe.org/2deo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2deo RCSB], [https://www.ebi.ac.uk/pdbsum/2deo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2deo 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=2deo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2deo OCA], [https://pdbe.org/2deo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2deo RCSB], [https://www.ebi.ac.uk/pdbsum/2deo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2deo ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | + | == Function == |
| | + | [https://www.uniprot.org/uniprot/STOPP_PYRHO STOPP_PYRHO] Protease that cleaves its substrates preferentially near hydrophobic or aromatic amino acid residues. Can degrade casein and the stomatin homolog PH1511 (in vitro).<ref>PMID:15611110</ref> <ref>PMID:16574150</ref> <ref>PMID:24121343</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | </StructureSection> | | </StructureSection> |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Pyrococcus horikoshii]] | + | [[Category: Pyrococcus horikoshii OT3]] |
| - | [[Category: Matsui, I]] | + | [[Category: Matsui I]] |
| - | [[Category: Yokoyama, H]] | + | [[Category: Yokoyama H]] |
| - | [[Category: Archaea]]
| + | |
| - | [[Category: Catalytic dyad]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Membrane protease]]
| + | |
| - | [[Category: Pyrococcus]]
| + | |
| - | [[Category: Specific for a stomatin homolog]]
| + | |
| - | [[Category: Thermostable]]
| + | |
| Structural highlights
Function
STOPP_PYRHO Protease that cleaves its substrates preferentially near hydrophobic or aromatic amino acid residues. Can degrade casein and the stomatin homolog PH1511 (in vitro).[1] [2] [3]
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 PubMed
Membrane-bound proteases are involved in various regulatory functions. Our previous study indicated that the N-terminal region of an open reading frame, PH1510 (residues 16-236, designated as 1510-N) from the hyperthermophilic archaeon Pyrococcus horikoshii, is a serine protease with a catalytic Ser-Lys dyad that specifically cleaves the C-terminal hydrophobic residues of a membrane protein, the stomatin-homolog PH1511. In humans, an absence of stomatin is associated with a form of hemolytic anemia known as hereditary stomatocytosis, but the function of stomatin is not fully understood. Here, we report the crystal structure of 1510-N in dimeric form. Each active site of 1510-N is rich in hydrophobic residues, which accounts for the substrate-specificity. The monomer of 1510-N shows structural similarity to one monomer of Escherichia coli ClpP, an ATP-dependent tetradecameric protease. But, their oligomeric forms are different. Major contributors to dimeric interaction in 1510-N are the alpha7 helix and beta9 strand, both of which are missing from ClpP. While the long handle region of ClpP contributes to the stacking of two heptameric rings, the corresponding L2 loop of 1510-N is disordered because the region has little interaction with other residues of the same molecule. The catalytic Ser97 of 1510-N is in almost the same location as the catalytic Ser97 of E.coli ClpP, whereas another residue, Lys138, presumably forming the catalytic dyad, is located in the disordered L2 region of 1510-N. These findings suggest that the binding of the substrate to the catalytic site of 1510-N induces conformational changes in a region that includes loop L2 so that Lys138 approaches the catalytic Ser97.
Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii.,Yokoyama H, Matsui E, Akiba T, Harata K, Matsui I J Mol Biol. 2006 May 12;358(4):1152-64. Epub 2006 Mar 9. PMID:16574150[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Yokoyama H, Matsui I. A novel thermostable membrane protease forming an operon with a stomatin homolog from the hyperthermophilic archaebacterium Pyrococcus horikoshii. J Biol Chem. 2005 Feb 25;280(8):6588-94. Epub 2004 Dec 16. PMID:15611110 doi:10.1074/jbc.M411748200
- ↑ Yokoyama H, Matsui E, Akiba T, Harata K, Matsui I. Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii. J Mol Biol. 2006 May 12;358(4):1152-64. Epub 2006 Mar 9. PMID:16574150 doi:10.1016/j.jmb.2006.02.052
- ↑ Yokoyama H, Kobayashi D, Takizawa N, Fujii S, Matsui I. Structural and biochemical analysis of a thermostable membrane-bound stomatin-specific protease. J Synchrotron Radiat. 2013 Nov;20(Pt 6):933-7. doi: 10.1107/S0909049513021328., Epub 2013 Sep 25. PMID:24121343 doi:http://dx.doi.org/10.1107/S0909049513021328
- ↑ Yokoyama H, Matsui E, Akiba T, Harata K, Matsui I. Molecular structure of a novel membrane protease specific for a stomatin homolog from the hyperthermophilic archaeon Pyrococcus horikoshii. J Mol Biol. 2006 May 12;358(4):1152-64. Epub 2006 Mar 9. PMID:16574150 doi:10.1016/j.jmb.2006.02.052
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