3dw0: Difference between revisions

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-{{Seed}}
-[[Image:3dw0.png|left|200px]]
-<!--
+==Crystal structure of the class A carbapenemase KPC-2 at 1.6 angstrom resolution==
-The line below this paragraph, containing "STRUCTURE_3dw0", creates the "Structure Box" on the page.
+<StructureSection load='3dw0' size='340' side='right'caption='[[3dw0]], [[Resolution|resolution]] 1.60&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'>[[3dw0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2ods 2ods]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DW0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3DW0 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]] 1.6&#8491;</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=3dw0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3dw0 OCA], [https://pdbe.org/3dw0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3dw0 RCSB], [https://www.ebi.ac.uk/pdbsum/3dw0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3dw0 ProSAT]</span></td></tr>
-{{STRUCTURE_3dw0|  PDB=3dw0  |  SCENE=  }}
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A8DS27_ECOLX A8DS27_ECOLX]
+== 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/dw/3dw0_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=3dw0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Two clinical strains of Escherichia coli (2138) and Enterobacter cloacae (7506) isolated from the same patient in France and showing resistance to extended-spectrum cephalosporins and low susceptibility to imipenem were investigated. Both strains harbored the plasmid-contained bla(TEM-1) and bla(KPC-2) genes. bla(KLUC-2), encoding a mutant of the chromosomal beta-lactamase of Kluyvera cryocrescens, was also identified at a plasmid location in E. cloacae 7506, suggesting the ISEcp1-assisted escape of bla(KLUC) from the chromosome. Determination of the KPC-2 structure at 1.6 A revealed that the binding site was occupied by the C-terminal (C-ter) residues coming from a symmetric KPC-2 monomer, with the ultimate C-ter Glu interacting with Ser130, Lys234, Thr235, and Thr237 in the active site. This mode of binding can be paralleled to the inhibition of the TEM-1 beta-lactamase by the inhibitory protein BLIP. Determination of the 1.23-A structure of a KPC-2 mutant in which the five C-ter residues were deleted revealed that the catalytic site was filled by a citrate molecule. Structure analysis and docking simulations with cefotaxime and imipenem provided further insights into the molecular basis of the extremely broad spectrum of KPC-2, which behaves as a cefotaximase with significant activity against carbapenems. In particular, residues 104, 105, 132, and 167 draw a binding cavity capable of accommodating both the aminothiazole moiety of cefotaxime and the 6 alpha-hydroxyethyl group of imipenem, with the binding of the former drug being also favored by a significant degree of freedom at the level of the loop at positions 96 to 105 and by an enlargement of the binding site at the end of strand beta 3.
-===Crystal structure of the class A carbapenemase KPC-2 at 1.6 angstrom resolution===
+Genetic and structural insights into the dissemination potential of the extremely broad-spectrum class A beta-lactamase KPC-2 identified in an Escherichia coli strain and an Enterobacter cloacae strain isolated from the same patient in France.,Petrella S, Ziental-Gelus N, Mayer C, Renard M, Jarlier V, Sougakoff W Antimicrob Agents Chemother. 2008 Oct;52(10):3725-36. Epub 2008 Jul 14. PMID:18625772<ref>PMID:18625772</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3dw0" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18625772}}, adds the Publication Abstract to the page
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18625772 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18625772}}
+__TOC__
+</StructureSection>
-==About this Structure==
-DW0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=2ods 2ods]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3DW0 OCA].
-==Reference==
-Genetic and structural insights into the dissemination potential of the extremely-broad-spectrum class A {beta}-lactamase (EBSBL) KPC-2 identified in two strains of Escherichia coli and Enterobacter cloacae isolated from the same patient in France., Petrella S, Ziental-Gelus N, Mayer C, Renard M, Jarlier V, Sougakoff W, Antimicrob Agents Chemother. 2008 Jul 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18625772 18625772]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Jarlier, V.]]
+[[Category: Jarlier V]]
-[[Category: Mayer, C.]]
+[[Category: Mayer C]]
-[[Category: Petrella, S.]]
+[[Category: Petrella S]]
-[[Category: Sougakoff, W.]]
+[[Category: Sougakoff W]]
-[[Category: Ziental-Gelus, N.]]
+[[Category: Ziental-Gelus N]]
-[[Category: Antibiotic resistance]]
-[[Category: Beta-lactamase]]
-[[Category: Carbapenemase]]
-[[Category: Hydrolase]]
-[[Category: Kpc-2]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Sep 17 13:08:17 2008''