2irv: Difference between revisions

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-[[Image:2irv.gif|left|200px]]
-<!--
+==Crystal structure of GlpG, a rhomboid intramembrane serine protease==
-The line below this paragraph, containing "STRUCTURE_2irv", creates the "Structure Box" on the page.
+<StructureSection load='2irv' size='340' side='right'caption='[[2irv]], [[Resolution|resolution]] 2.30&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'>[[2irv]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. The August 2011 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Rhomboid Protease GlpG''  by David Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2011_8 10.2210/rcsb_pdb/mom_2011_8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IRV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IRV 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]] 2.3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PGV:(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+(11E)-OCTADEC-11-ENOATE'>PGV</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_2irv|  PDB=2irv  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2irv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2irv OCA], [https://pdbe.org/2irv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2irv RCSB], [https://www.ebi.ac.uk/pdbsum/2irv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2irv 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>
+== 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/ir/2irv_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=2irv ConSurf].
+<div style="clear:both"></div>
-'''Crystal structure of GlpG, a rhomboid intramembrane serine protease'''
+==See Also==
+*[[Rhomboid protease|Rhomboid protease]]
+== References ==
-==Overview==
+<references/>
-Intramembrane proteases catalyze peptide bond cleavage of integral membrane protein substrates. This activity is crucial for many biological and pathological processes. Rhomboids are evolutionarily widespread intramembrane serine proteases. Here, we present the 2.3-A-resolution crystal structure of a rhomboid from Escherichia coli. The enzyme has six transmembrane helices, five of which surround a short TM4, which starts deep within the membrane at the catalytic serine residue. Thus, the catalytic serine is in an externally exposed cavity, which provides a hydrophilic environment for proteolysis. Our results reveal a mechanism to enable water-dependent catalysis at the depth of the hydrophobic milieu of the membrane and suggest how substrates gain access to the sequestered rhomboid active site.
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-IRV is a [[Single protein]] structure of 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=2IRV OCA].
+[[Category: Large Structures]]
+[[Category: RCSB PDB Molecule of the Month]]
-==Reference==
+[[Category: Rhomboid Protease GlpG]]
-Structural basis for intramembrane proteolysis by rhomboid serine proteases., Ben-Shem A, Fass D, Bibi E, Proc Natl Acad Sci U S A. 2007 Jan 9;104(2):462-6. Epub 2006 Dec 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17190827 17190827]
+[[Category: Ben-Shem A]]
-[[Category: Escherichia coli]]
+[[Category: Bibi E]]
-[[Category: Single protein]]
+[[Category: Fass D]]
-[[Category: Ben-Shem, A.]]
-[[Category: Bibi, E.]]
-[[Category: Fass, D.]]
-[[Category: Cavity]]
-[[Category: Membrane protein]]
-[[Category: Ser-his dyad]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 07:47:29 2008''