1fq5: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1fq5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FQ5 FirstGlance]. <br>
<table><tr><td colspan='2'>[[1fq5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1FQ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1FQ5 FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0GM:N-[(5S,9S,10S,13S)-9-HYDROXY-5,10-BIS(2-METHYLPROPYL)-4,7,12,16-TETRAOXO-3,6,11,17-TETRAAZABICYCLO[17.3.1]TRICOSA-1(23),19,21-TRIEN-13-YL]-3-(NAPHTHALEN-1-YL)-2-(NAPHTHALEN-1-YLMETHYL)PROPANAMIDE'>0GM</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</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]] 2.4&#8491;</td></tr>
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2jxr|2jxr]], [[1dpj|1dpj]], [[1fq4|1fq4]], [[1fq6|1fq6]], [[1fq7|1fq7]], [[1fq8|1fq8]]</div></td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=0GM:N-[(5S,9S,10S,13S)-9-HYDROXY-5,10-BIS(2-METHYLPROPYL)-4,7,12,16-TETRAOXO-3,6,11,17-TETRAAZABICYCLO[17.3.1]TRICOSA-1(23),19,21-TRIEN-13-YL]-3-(NAPHTHALEN-1-YL)-2-(NAPHTHALEN-1-YLMETHYL)PROPANAMIDE'>0GM</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</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'>[https://en.wikipedia.org/wiki/Saccharopepsin Saccharopepsin], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.4.23.25 3.4.23.25] </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=1fq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fq5 OCA], [https://pdbe.org/1fq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fq5 RCSB], [https://www.ebi.ac.uk/pdbsum/1fq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fq5 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=1fq5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1fq5 OCA], [https://pdbe.org/1fq5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1fq5 RCSB], [https://www.ebi.ac.uk/pdbsum/1fq5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1fq5 ProSAT]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[https://www.uniprot.org/uniprot/CARP_YEAST CARP_YEAST]] Aspartyl protease implicated in the post-translational regulation of S.cerevisiae vacuolar proteinases. Acts on YSCB, on YSCY and on itself.  
[https://www.uniprot.org/uniprot/CARP_YEAST CARP_YEAST] Aspartyl protease implicated in the post-translational regulation of S.cerevisiae vacuolar proteinases. Acts on YSCB, on YSCY and on itself.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
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</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=1fq5 ConSurf].
</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=1fq5 ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Saccharopepsin is a vacuolar aspartic proteinase involved in activation of a number of hydrolases. The enzyme has great structural homology to mammalian aspartic proteinases including human renin and we have used it as a model system to study the binding of renin inhibitors by X-ray crystallography. Five medium-to-high resolution structures of saccharopepsin complexed with transition-state analogue renin inhibitors were determined. The structure of a cyclic peptide inhibitor (PD-129,541) complexed with the proteinase was solved to 2.5 A resolution. This inhibitor has low affinity for human renin yet binds very tightly to the yeast proteinase (K(i)=4 nM). The high affinity of this inhibitor can be attributed to its bulky cyclic moiety spanning P(2)-P(3)' and other residues that appear to optimally fit the binding sub-sites of the enzyme. Superposition of the saccharopepsin structure on that of renin showed that a movement of the loop 286-301 relative to renin facilitates tighter binding of this inhibitor to saccharopepsin. Our 2.8 A resolution structure of the complex with CP-108,420 shows that its benzimidazole P(3 )replacement retains one of the standard hydrogen bonds that normally involve the inhibitor's main-chain. This suggests a non-peptide lead in overcoming the problem of susceptible peptide bonds in the design of aspartic proteinase inhibitors. CP-72,647 which possesses a basic histidine residue at P(2), has a high affinity for renin (K(i)=5 nM) but proves to be a poor inhibitor for saccharopepsin (K(i)=3.7 microM). This may stem from the fact that the histidine residue would not bind favourably with the predominantly hydrophobic S(2) sub-site of saccharopepsin.
X-ray structures of five renin inhibitors bound to saccharopepsin: exploration of active-site specificity.,Cronin NB, Badasso MO, J Tickle I, Dreyer T, Hoover DJ, Rosati RL, Humblet CC, Lunney EA, Cooper JB J Mol Biol. 2000 Nov 10;303(5):745-60. PMID:11061973<ref>PMID:11061973</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1fq5" style="background-color:#fffaf0;"></div>


==See Also==
==See Also==
*[[Pepsin|Pepsin]]
*[[Pepsin|Pepsin]]
*[[Proteinase 3D structures|Proteinase 3D structures]]
*[[Proteinase 3D structures|Proteinase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharopepsin]]
[[Category: Badasso MO]]
[[Category: Badasso, M O]]
[[Category: Cooper JB]]
[[Category: Cooper, J B]]
[[Category: Cronin NB]]
[[Category: Cronin, N B]]
[[Category: Dreyer T]]
[[Category: Dreyer, T]]
[[Category: Hoover DJ]]
[[Category: Hoover, D J]]
[[Category: Humblet CC]]
[[Category: Humblet, C C]]
[[Category: Lunney EA]]
[[Category: Lunney, E A]]
[[Category: Rosati RL]]
[[Category: Rosati, R L]]
[[Category: Tickle IJ]]
[[Category: Tickle, I J]]
[[Category: Hydrolase-hydrolase inhibitor complex]]

Revision as of 11:15, 27 March 2024

X-ray structure of a cyclic statine inhibitor PD-129,541 bound to yeast proteinase A

1fq5, resolution 2.40Å

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