2jxr: Difference between revisions

From Proteopedia
Jump to navigationJump to search
← Older edit
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
OCA (talk | contribs)
Bots, Bureaucrats, journal, Administrators
3,331,613 edits
No edit summary
 
(11 intermediate revisions by the same user not shown)
Line 1: Line 1:
[[Image:2jxr.gif|left|200px]]
<!--
The line below this paragraph, containing "STRUCTURE_2jxr", creates the "Structure Box" on the page.
You may change the PDB parameter (which sets the PDB file loaded into the applet)
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
or leave the SCENE parameter empty for the default display.
-->
{{STRUCTURE_2jxr|  PDB=2jxr  |  SCENE=  }}
'''STRUCTURE OF YEAST PROTEINASE A'''


==STRUCTURE OF YEAST PROTEINASE A==
<StructureSection load='2jxr' size='340' side='right'caption='[[2jxr]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[2jxr]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jxr 1jxr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JXR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JXR FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2Z3:N-(MORPHOLIN-4-YLCARBONYL)-L-PHENYLALANYL-N-[(1R)-1-(CYCLOHEXYLMETHYL)-3,3-DIFLUORO-2,2-DIHYDROXY-4-(METHYLAMINO)-4-OXOBUTYL]-L-NORLEUCINAMIDE'>2Z3</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>
<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=2jxr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jxr OCA], [https://pdbe.org/2jxr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jxr RCSB], [https://www.ebi.ac.uk/pdbsum/2jxr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jxr ProSAT]</span></td></tr>
</table>
== 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.
== 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/jx/2jxr_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=2jxr ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structures of glycosylated native proteinase A, an aspartic proteinase found in the vacuole of Saccharomyces cerevisiae, and its complex with a difluorostatone-containing tripeptide have been determined by molecular replacement to 3.5 A and 2.4 A resolutions, respectively. Superposition of the bound and native forms gave an r.m.s. difference of 0.6 A largely reflecting the poor resolution of the native crystal structure. The secondary and tertiary structures are highly similar to those found in porcine pepsin and lysosomal cathepsin D; superposition of the structure of proteinase A bound to the difluorostatone inhibitor on those of pepsin and cathepsin D gave pairwise r.m.s. differences for C(alpha) atoms of 1.36 A and 0.88 A. Most differences occur in loop regions. Comparison of the structure of the proteinase A-difluorostatone complex with that of endothiapepsin bound with the same inhibitor shows that the conformation and hydrogen bond interactions of the inhibitor in the active site are very similar, even though the enzymes have only 27% sequence identity. Electron density for the crystal structure of the proteinase A complex reveals five residues of the oligosaccharide structure attached to Asn67: Man-(1 --&gt; 2)-alpha-Man-(1 --&gt; 3)-beta-Man-(1 --&gt; 4)-beta-GlcNAc-(1 --&gt; 4)-beta-GlcNAc-Asn-67. The first three residues of the oligosaccharide cover the same region of the protein surface as those of the oligosaccharide attached to the equivalent position in cathepsin D. The second carbohydrate attachment site is disordered beyond the first carbohydrate residue in both enzymes.


==Overview==
The three-dimensional structure at 2.4 A resolution of glycosylated proteinase A from the lysosome-like vacuole of Saccharomyces cerevisiae.,Aguilar CF, Cronin NB, Badasso M, Dreyer T, Newman MP, Cooper JB, Hoover DJ, Wood SP, Johnson MS, Blundell TL J Mol Biol. 1997 Apr 11;267(4):899-915. PMID:9135120<ref>PMID:9135120</ref>
The crystal structures of glycosylated native proteinase A, an aspartic proteinase found in the vacuole of Saccharomyces cerevisiae, and its complex with a difluorostatone-containing tripeptide have been determined by molecular replacement to 3.5 A and 2.4 A resolutions, respectively. Superposition of the bound and native forms gave an r.m.s. difference of 0.6 A largely reflecting the poor resolution of the native crystal structure. The secondary and tertiary structures are highly similar to those found in porcine pepsin and lysosomal cathepsin D; superposition of the structure of proteinase A bound to the difluorostatone inhibitor on those of pepsin and cathepsin D gave pairwise r.m.s. differences for C(alpha) atoms of 1.36 A and 0.88 A. Most differences occur in loop regions. Comparison of the structure of the proteinase A-difluorostatone complex with that of endothiapepsin bound with the same inhibitor shows that the conformation and hydrogen bond interactions of the inhibitor in the active site are very similar, even though the enzymes have only 27% sequence identity. Electron density for the crystal structure of the proteinase A complex reveals five residues of the oligosaccharide structure attached to Asn67: Man-(1 --&gt; 2)-alpha-Man-(1 --&gt; 3)-beta-Man-(1 --&gt; 4)-beta-GlcNAc-(1 --&gt; 4)-beta-GlcNAc-Asn-67. The first three residues of the oligosaccharide cover the same region of the protein surface as those of the oligosaccharide attached to the equivalent position in cathepsin D. The second carbohydrate attachment site is disordered beyond the first carbohydrate residue in both enzymes.


==About this Structure==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
2JXR is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1jxr 1jxr]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JXR OCA].
</div>
<div class="pdbe-citations 2jxr" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
The three-dimensional structure at 2.4 A resolution of glycosylated proteinase A from the lysosome-like vacuole of Saccharomyces cerevisiae., Aguilar CF, Cronin NB, Badasso M, Dreyer T, Newman MP, Cooper JB, Hoover DJ, Wood SP, Johnson MS, Blundell TL, J Mol Biol. 1997 Apr 11;267(4):899-915. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9135120 9135120]
*[[Pepsin|Pepsin]]
[[Category: Saccharomyces cerevisiae]]
*[[Proteinase|Proteinase]]
*[[Proteinase 3D structures|Proteinase 3D structures]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Atcc 18824]]
[[Category: Large Structures]]
[[Category: Saccharopepsin]]
[[Category: Saccharopepsin]]
[[Category: Single protein]]
[[Category: Aguilar, C F]]
[[Category: Aguilar, C F.]]
[[Category: Badasso, M]]
[[Category: Badasso, M.]]
[[Category: Blundell, T L]]
[[Category: Blundell, T L.]]
[[Category: Cooper, J B]]
[[Category: Cooper, J B.]]
[[Category: Cronin, N B]]
[[Category: Cronin, N B.]]
[[Category: Dreyer, T]]
[[Category: Dreyer, T.]]
[[Category: Hoover, D J]]
[[Category: Hoover, D J.]]
[[Category: Johnson, M S]]
[[Category: Johnson, M S.]]
[[Category: Newman, M P]]
[[Category: Newman, M P.]]
[[Category: Wood, S P]]
[[Category: Wood, S P.]]
[[Category: Aspartyl protease]]
[[Category: Aspartyl protease]]
[[Category: Glycoprotein]]
[[Category: Glycoprotein]]
[[Category: Hydrolase]]
[[Category: Hydrolase-hydrolase inhibitor complex]]
[[Category: Signal]]
[[Category: Zymogen]]
[[Category: Zymogen]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 09:23:04 2008''
Retrieved from "https://proteopedia.org/2jxr"