1ko3: Difference between revisions

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-[[Image:1ko3.gif|left|200px]]
- {{Structure
+==VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa with Cys221 reduced==
-|PDB= 1ko3 |SIZE=350|CAPTION= <scene name='initialview01'>1ko3</scene>, resolution 1.91&Aring;
+<StructureSection load='1ko3' size='340' side='right'caption='[[1ko3]], [[Resolution|resolution]] 1.91&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene>
+<table><tr><td colspan='2'>[[1ko3]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KO3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1KO3 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Beta-lactamase Beta-lactamase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.2.6 3.5.2.6] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.91&#8491;</td></tr>
-|GENE= blaVIM-2 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=287 Pseudomonas aeruginosa])
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-|DOMAIN=
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ko3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ko3 OCA], [https://pdbe.org/1ko3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ko3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ko3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ko3 ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1ko2|1KO2]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ko3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ko3 OCA], [http://www.ebi.ac.uk/pdbsum/1ko3 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ko3 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/Q9K2N0_PSEAI Q9K2N0_PSEAI]
+== 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/ko/1ko3_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=1ko3 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The crystal structures of the universally widespread metallo-beta-lactamase (MBL) Verona integron-encoded MBL (VIM)-2 from Pseudomonas aeruginosa have been solved in their native form as well as in an unexpected oxidised form. This carbapenem-hydrolysing enzyme belongs to the so-called B1 subfamily of MBLs and shares the folding of alpha beta/beta alpha sandwich, consisting of a core of beta-sheet surrounded by alpha-helices. Surprisingly, it showed a high tendency to be strongly oxidised at the catalytic cysteine located in the Cys site, Cys221, which, in the oxidised structure, becomes a cysteinesulfonic residue. Its native structure was obtained only in the presence of Tris(2-carboxyethyl)phosphine. This oxidation might be a consequence of a lower affinity for the second Zn located in the Cys site that would also explain the observed susceptibility of VIM-2 to chelating agents. This modification, if present in nature, might play a role in catalytic down-regulation. Comparison between native and oxidised VIM-2 and a predicted model of VIM-1 (which shows one residue different in the Cys site compared with VIM-2) is performed to explain the different activities and antibiotic specificities.
-'''VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa with Cys221 reduced'''
+The three-dimensional structure of VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa in its reduced and oxidised form.,Garcia-Saez I, Docquier JD, Rossolini GM, Dideberg O J Mol Biol. 2008 Jan 18;375(3):604-11. Epub 2007 Nov 13. PMID:18061205<ref>PMID:18061205</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1ko3" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The crystal structures of the universally widespread metallo-beta-lactamase (MBL) Verona integron-encoded MBL (VIM)-2 from Pseudomonas aeruginosa have been solved in their native form as well as in an unexpected oxidised form. This carbapenem-hydrolysing enzyme belongs to the so-called B1 subfamily of MBLs and shares the folding of alpha beta/beta alpha sandwich, consisting of a core of beta-sheet surrounded by alpha-helices. Surprisingly, it showed a high tendency to be strongly oxidised at the catalytic cysteine located in the Cys site, Cys221, which, in the oxidised structure, becomes a cysteinesulfonic residue. Its native structure was obtained only in the presence of Tris(2-carboxyethyl)phosphine. This oxidation might be a consequence of a lower affinity for the second Zn located in the Cys site that would also explain the observed susceptibility of VIM-2 to chelating agents. This modification, if present in nature, might play a role in catalytic down-regulation. Comparison between native and oxidised VIM-2 and a predicted model of VIM-1 (which shows one residue different in the Cys site compared with VIM-2) is performed to explain the different activities and antibiotic specificities.
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-KO3 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_aeruginosa Pseudomonas aeruginosa]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1KO3 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-The three-dimensional structure of VIM-2, a Zn-beta-lactamase from Pseudomonas aeruginosa in its reduced and oxidised form., Garcia-Saez I, Docquier JD, Rossolini GM, Dideberg O, J Mol Biol. 2008 Jan 18;375(3):604-11. Epub 2007 Nov 13. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18061205 18061205]
-[[Category: Beta-lactamase]]
 [[Category: Pseudomonas aeruginosa]]
-[[Category: Single protein]]
+[[Category: Dideberg O]]
-[[Category: Dideberg, O.]]
+[[Category: Docquier J-D]]
-[[Category: Docquier, J D.]]
+[[Category: Garcia-Saez I]]
-[[Category: Garcia-Saez, I.]]
+[[Category: Rossolini GM]]
-[[Category: Rossolini, G M.]]
-[[Category: alpha-beta/beta-alpha fold]]
-[[Category: hydrolase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:51:12 2008''