1ssx: Difference between revisions

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-[[Image:1ssx.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1ssx", 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.
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-{{STRUCTURE_1ssx|  PDB=1ssx  |  SCENE=  }}
-'''0.83A resolution crystal structure of alpha-lytic protease at pH 8'''
+==0.83A resolution crystal structure of alpha-lytic protease at pH 8==
+<StructureSection load='1ssx' size='340' side='right'caption='[[1ssx]], [[Resolution|resolution]] 0.83&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ssx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SSX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1SSX FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 0.83&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1ssx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ssx OCA], [https://pdbe.org/1ssx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ssx RCSB], [https://www.ebi.ac.uk/pdbsum/1ssx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ssx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PRLA_LYSEN PRLA_LYSEN]
+== 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/ss/1ssx_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1ssx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structure of the extracellular bacterial serine protease alpha-lytic protease (alphaLP) has been solved at 0.83 A resolution at pH 8. This ultra-high resolution structure allows accurate analysis of structural elements not possible with previous structures. Hydrogen atoms are visible, and confirm active-site hydrogen-bonding interactions expected for the apo enzyme. In particular, His57 N(delta1) participates in a normal hydrogen bond with Asp102 in the catalytic triad, with a hydrogen atom visible 0.83(+/-0.06)A from the His N(delta1). The catalytic Ser195 occupies two conformations, one corresponding to a population of His57 that is doubly protonated, the other to the singly protonated His57. Based on the occupancy of these conformations, the pKa of His57 is calculated to be approximately 8.8 when a sulfate ion occupies the active site. This 0.83 A structure has allowed critical analysis of geometric distortions within the structure. Interestingly, Phe228 is significantly distorted from planarity. The distortion of Phe228, buried in the core of the C-terminal domain, occurs at an estimated energetic cost of 4.1 kcal/mol. The conformational space for Phe228 is severely limited by the presence of Trp199, which prevents Phe228 from adopting the rotamer observed in many other chymotrypsin family members. In alphaLP, the only allowed rotamer leads to the deformation of Phe228 due to steric interactions with Thr181. We hypothesize that tight packing of co-evolved residues in this region, and the subsequent deformation of Phe228, contributes to the high cooperativity and large energetic barriers for folding and unfolding of alphaLP. The kinetic stability imparted by the large, cooperative unfolding barrier plays a critical role in extending the lifetime of the protease in its harsh environment.
-==Overview==
+The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain.,Fuhrmann CN, Kelch BA, Ota N, Agard DA J Mol Biol. 2004 May 14;338(5):999-1013. PMID:15111063<ref>PMID:15111063</ref>
-The crystal structure of the extracellular bacterial serine protease alpha-lytic protease (alphaLP) has been solved at 0.83 A resolution at pH 8. This ultra-high resolution structure allows accurate analysis of structural elements not possible with previous structures. Hydrogen atoms are visible, and confirm active-site hydrogen-bonding interactions expected for the apo enzyme. In particular, His57 N(delta1) participates in a normal hydrogen bond with Asp102 in the catalytic triad, with a hydrogen atom visible 0.83(+/-0.06)A from the His N(delta1). The catalytic Ser195 occupies two conformations, one corresponding to a population of His57 that is doubly protonated, the other to the singly protonated His57. Based on the occupancy of these conformations, the pKa of His57 is calculated to be approximately 8.8 when a sulfate ion occupies the active site. This 0.83 A structure has allowed critical analysis of geometric distortions within the structure. Interestingly, Phe228 is significantly distorted from planarity. The distortion of Phe228, buried in the core of the C-terminal domain, occurs at an estimated energetic cost of 4.1 kcal/mol. The conformational space for Phe228 is severely limited by the presence of Trp199, which prevents Phe228 from adopting the rotamer observed in many other chymotrypsin family members. In alphaLP, the only allowed rotamer leads to the deformation of Phe228 due to steric interactions with Thr181. We hypothesize that tight packing of co-evolved residues in this region, and the subsequent deformation of Phe228, contributes to the high cooperativity and large energetic barriers for folding and unfolding of alphaLP. The kinetic stability imparted by the large, cooperative unfolding barrier plays a critical role in extending the lifetime of the protease in its harsh environment.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-SSX is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Lysobacter_enzymogenes Lysobacter enzymogenes]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SSX OCA].
+</div>
+<div class="pdbe-citations 1ssx" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-The 0.83 A resolution crystal structure of alpha-lytic protease reveals the detailed structure of the active site and identifies a source of conformational strain., Fuhrmann CN, Kelch BA, Ota N, Agard DA, J Mol Biol. 2004 May 14;338(5):999-1013. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15111063 15111063]
+*[[Alpha-lytic protease 3D structures|Alpha-lytic protease 3D structures]]
-[[Category: Alpha-lytic endopeptidase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Lysobacter enzymogenes]]
-[[Category: Single protein]]
+[[Category: Agard DA]]
-[[Category: Agard, D A.]]
+[[Category: Fuhrmann CN]]
-[[Category: Fuhrmann, C N.]]
-[[Category: A-lytic protease]]
-[[Category: Packing distortion]]
-[[Category: Protein folding]]
-[[Category: Protein stability]]
-[[Category: Serine protease]]
-[[Category: Ultra-high resolution]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 09:06:10 2008''