1iyp: Difference between revisions

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-[[Image:1iyp.jpg|left|200px]]
- {{Structure
+==Toho-1 beta-Lactamase In Complex With Cephalothin==
-|PDB= 1iyp |SIZE=350|CAPTION= <scene name='initialview01'>1iyp</scene>, resolution 2.&Aring;
+<StructureSection load='1iyp' size='340' side='right'caption='[[1iyp]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=CEP:CEPHALOTHIN+GROUP'>CEP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
+<table><tr><td colspan='2'>[[1iyp]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IYP 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]] 2&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CEP:CEPHALOTHIN+GROUP'>CEP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1iyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iyp OCA], [https://pdbe.org/1iyp PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iyp RCSB], [https://www.ebi.ac.uk/pdbsum/1iyp PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iyp ProSAT]</span></td></tr>
-|RELATEDENTRY=[[1iyo|1IYO]], [[1iyq|1IYQ]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iyp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iyp OCA], [http://www.ebi.ac.uk/pdbsum/1iyp PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1iyp RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/BLT1_ECOLX BLT1_ECOLX] Has strong cefotaxime-hydrolyzing activity.
+== 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/iy/1iyp_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1iyp ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Bacterial resistance to beta-lactam antibiotics is a serious problem limiting current clinical therapy. The most common form of resistance is the production of beta-lactamases that inactivate beta-lactam antibiotics. Toho-1 is an extended-spectrum beta-lactamase that has acquired efficient activity not only to penicillins but also to cephalosporins including the expanded-spectrum cephalosporins that were developed to be stable in former beta-lactamases. We present the acyl-intermediate structures of Toho-1 in complex with cefotaxime (expanded-spectrum cephalosporin), cephalothin (non-expanded-spectrum cephalosporin), and benzylpenicillin at 1.8-, 2.0-, and 2.1-A resolutions, respectively. These structures reveal distinct features that can explain the ability of Toho-1 to hydrolyze expanded-spectrum cephalosporins. First, the Omega-loop of Toho-1 is displaced to avoid the steric contacts with the bulky side chain of cefotaxime. Second, the conserved residues Asn(104) and Asp(240) form unique interactions with the bulky side chain of cefotaxime to fix it tightly. Finally, the unique interaction between the conserved Ser(237) and cephalosporins probably helps to bring the beta-lactam carbonyl group to the suitable position in the oxyanion hole, thus increasing the cephalosporinase activity.
-'''Toho-1 beta-Lactamase In Complex With Cephalothin'''
+Acyl-intermediate structures of the extended-spectrum class A beta-lactamase, Toho-1, in complex with cefotaxime, cephalothin, and benzylpenicillin.,Shimamura T, Ibuka A, Fushinobu S, Wakagi T, Ishiguro M, Ishii Y, Matsuzawa H J Biol Chem. 2002 Nov 29;277(48):46601-8. Epub 2002 Sep 8. PMID:12221102<ref>PMID:12221102</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1iyp" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-Bacterial resistance to beta-lactam antibiotics is a serious problem limiting current clinical therapy. The most common form of resistance is the production of beta-lactamases that inactivate beta-lactam antibiotics. Toho-1 is an extended-spectrum beta-lactamase that has acquired efficient activity not only to penicillins but also to cephalosporins including the expanded-spectrum cephalosporins that were developed to be stable in former beta-lactamases. We present the acyl-intermediate structures of Toho-1 in complex with cefotaxime (expanded-spectrum cephalosporin), cephalothin (non-expanded-spectrum cephalosporin), and benzylpenicillin at 1.8-, 2.0-, and 2.1-A resolutions, respectively. These structures reveal distinct features that can explain the ability of Toho-1 to hydrolyze expanded-spectrum cephalosporins. First, the Omega-loop of Toho-1 is displaced to avoid the steric contacts with the bulky side chain of cefotaxime. Second, the conserved residues Asn(104) and Asp(240) form unique interactions with the bulky side chain of cefotaxime to fix it tightly. Finally, the unique interaction between the conserved Ser(237) and cephalosporins probably helps to bring the beta-lactam carbonyl group to the suitable position in the oxyanion hole, thus increasing the cephalosporinase activity.
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-IYP 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=1IYP OCA].
+__TOC__
+</StructureSection>
-==Reference==
-Acyl-intermediate structures of the extended-spectrum class A beta-lactamase, Toho-1, in complex with cefotaxime, cephalothin, and benzylpenicillin., Shimamura T, Ibuka A, Fushinobu S, Wakagi T, Ishiguro M, Ishii Y, Matsuzawa H, J Biol Chem. 2002 Nov 29;277(48):46601-8. Epub 2002 Sep 8. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12221102 12221102]
-[[Category: Beta-lactamase]]
 [[Category: Escherichia coli]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Fushinobu, S.]]
+[[Category: Fushinobu S]]
-[[Category: Ibuka, A.]]
+[[Category: Ibuka A]]
-[[Category: Ishiguro, M.]]
+[[Category: Ishiguro M]]
-[[Category: Ishii, Y.]]
+[[Category: Ishii Y]]
-[[Category: Matsuzawa, H.]]
+[[Category: Matsuzawa H]]
-[[Category: Shimamura, T.]]
+[[Category: Shimamura T]]
-[[Category: Wakagi, T.]]
+[[Category: Wakagi T]]
-[[Category: acyl-enzyme]]
-[[Category: beta-lactamase]]
-[[Category: cephalothin]]
-[[Category: complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:26:31 2008''