3ubb: Difference between revisions

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-[[Image:3ubb.jpg|left|200px]]
-<!--
+==The crystal structure of GlpG in complex with a phosphonofluoridate inhibitor==
-The line below this paragraph, containing "STRUCTURE_3ubb", creates the "Structure Box" on the page.
+<StructureSection load='3ubb' size='340' side='right'caption='[[3ubb]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3ubb]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3UBB FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.601&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3UB:PROPAN-2-YL+HYDROGEN+(S)-[(1R)-1-{[(BENZYLOXY)CARBONYL]AMINO}ETHYL]PHOSPHONATE'>3UB</scene></td></tr>
-{{STRUCTURE_3ubb|  PDB=3ubb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ubb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ubb OCA], [https://pdbe.org/3ubb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ubb RCSB], [https://www.ebi.ac.uk/pdbsum/3ubb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ubb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/GLPG_ECOLI GLPG_ECOLI] Rhomboid-type serine protease that catalyzes intramembrane proteolysis.<ref>PMID:17099694</ref> <ref>PMID:16216077</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Rhomboid protease conducts proteolysis inside the hydrophobic environment of the membrane. The conformational flexibility of the protease is essential for the enzyme mechanism, but the nature of this flexibility is not completely understood. Here we describe the crystal structure of rhomboid protease GlpG in complex with a phosphonofluoridate inhibitor, which is covalently bonded to the catalytic serine and extends into the S' side of the substrate binding cleft. Inhibitor binding causes subtle but extensive changes in the membrane protease. Many transmembrane helices tilt and shift positions, and the gap between S2 and S5 is slightly widened so that the inhibitor can bind between them. The side chain of Phe-245 from a loop (L5) that acts as a cap rotates and uncovers the opening of the substrate binding cleft to the lipid bilayer. A concurrent turn of the polypeptide backbone at Phe-245 moves the rest of the cap and exposes the catalytic serine to the aqueous solution. This study, together with earlier crystallographic investigation of smaller inhibitors, suggests a simple model for explaining substrate binding to rhomboid protease.
-===The crystal structure of GlpG in complex with a phosphonofluoridate inhibitor===
+Conformational Change in Rhomboid Protease GlpG Induced by Inhibitor Binding to Its S' Subsites.,Xue Y, Chowdhury S, Liu X, Akiyama Y, Ellman J, Ha Y Biochemistry. 2012 May 8;51(18):3723-31. Epub 2012 Apr 24. PMID:22515733<ref>PMID:22515733</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ubb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_22515733}}, adds the Publication Abstract to the page
+*[[Rhomboid protease|Rhomboid protease]]
-(as it appears on PubMed at http://www.pubmed.gov), where 22515733 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_22515733}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-[[3ubb]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3UBB OCA].
+[[Category: Large Structures]]
+[[Category: Ha Y]]
-==Reference==
+[[Category: Xue Y]]
-<ref group="xtra">PMID:022515733</ref><references group="xtra"/>
-[[Category: Escherichia coli]]
-[[Category: Rhomboid protease]]
-[[Category: Ha, Y.]]
-[[Category: Xue, Y.]]
-[[Category: Helix bundle]]
-[[Category: Hydrolase-inhibitor complex]]
-[[Category: Membrane]]