2qmi: Difference between revisions

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 <StructureSection load='2qmi' size='340' side='right'caption='[[2qmi]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2qmi]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/"pyrococcus_abyssi"_erauso_et_al._1993 "pyrococcus abyssi" erauso et al. 1993]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QMI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2qmi]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QMI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QMI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DO3:10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE+1,4,7-TRIACETIC+ACID'>DO3</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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]] 2.2&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">pbp ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=29292 "Pyrococcus abyssi" Erauso et al. 1993])</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DO3:10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE+1,4,7-TRIACETIC+ACID'>DO3</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </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=2qmi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qmi OCA], [https://pdbe.org/2qmi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qmi RCSB], [https://www.ebi.ac.uk/pdbsum/2qmi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qmi ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q9V2D6_PYRAB Q9V2D6_PYRAB]
 == Evolutionary Conservation ==
 [[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=2qmi ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Self-compartmentalizing proteases orchestrate protein turnover through an original architecture characterized by a central catalytic chamber. Here we report the first structure of an archaeal member of a new self-compartmentalizing protease family forming a cubic-shaped octamer with D(4) symmetry and referred to as CubicO. We solved the structure of the Pyrococcus abyssi Pab87 protein at 2.2 A resolution using the anomalous signal of the high-phasing-power lanthanide derivative Lu-HPDO3A. A 20 A wide channel runs through this supramolecular assembly of 0.4 MDa, giving access to a 60 A wide central chamber holding the eight active sites. Surprisingly, activity assays revealed that Pab87 degrades specifically d-amino acid containing peptides, which have never been observed in archaea. Genomic context of the Pab87 gene showed that it is surrounded by genes involved in the amino acid/peptide transport or metabolism. We propose that CubicO proteases are involved in the processing of d-peptides from environmental origins.
-Structure of the archaeal pab87 peptidase reveals a novel self-compartmentalizing protease family.,Delfosse V, Girard E, Birck C, Delmarcelle M, Delarue M, Poch O, Schultz P, Mayer C PLoS One. 2009;4(3):e4712. Epub 2009 Mar 5. PMID:19266066<ref>PMID:19266066</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 2qmi" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Pyrococcus abyssi erauso et al. 1993]]
-[[Category: Beta-lactamase]]
 [[Category: Large Structures]]
-[[Category: Delfosse, V]]
+[[Category: Pyrococcus abyssi]]
-[[Category: Girard, E]]
+[[Category: Delfosse V]]
-[[Category: Mayer, C]]
+[[Category: Girard E]]
-[[Category: Moulinier, L]]
+[[Category: Mayer C]]
-[[Category: Schultz, P]]
+[[Category: Moulinier L]]
-[[Category: Archaea]]
+[[Category: Schultz P]]
-[[Category: Hydrolase]]
-[[Category: Lu-hpdo3a]]
-[[Category: Octamer]]
-[[Category: Pab87]]
-[[Category: Pbp]]