3c4o: Difference between revisions

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OCA

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-[[Image:3c4o.jpg|left|200px]]
-<!--
+==Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) E73M/S130K/S146M complex==
-The line below this paragraph, containing "STRUCTURE_3c4o", creates the "Structure Box" on the page.
+<StructureSection load='3c4o' size='340' side='right'caption='[[3c4o]], [[Resolution|resolution]] 1.70&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'>[[3c4o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae] and [https://en.wikipedia.org/wiki/Streptomyces_clavuligerus Streptomyces clavuligerus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C4O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3C4O 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]] 1.7&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3c4o|  PDB=3c4o  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3c4o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3c4o OCA], [https://pdbe.org/3c4o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3c4o RCSB], [https://www.ebi.ac.uk/pdbsum/3c4o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3c4o ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/BLA1_KLEPN BLA1_KLEPN]
+== 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/c4/3c4o_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=3c4o ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Beta-lactamases are enzymes that catalyze the hydrolysis of beta-lactam antibiotics. beta-lactamase/beta-lactamase inhibitor protein (BLIP) complexes are emerging as a well characterized experimental model system for studying protein-protein interactions. BLIP is a 165 amino acid protein that inhibits several class A beta-lactamases with a wide range of affinities: picomolar affinity for K1; nanomolar affinity for TEM-1, SME-1, and BlaI; but only micromolar affinity for SHV-1 beta-lactamase. The large differences in affinity coupled with the availability of extensive mutagenesis data and high-resolution crystal structures for the TEM-1/BLIP and SHV-1/BLIP complexes make them attractive systems for the further development of computational design methodology. We used EGAD, a physics-based computational design program, to redesign BLIP in an attempt to increase affinity for SHV-1. Characterization of several of designs and point mutants revealed that in all cases, the mutations stabilize the interface by 10- to 1000-fold relative to wild type BLIP. The calculated changes in binding affinity for the mutants were within a mean absolute error of 0.87 kcal/mol from the experimental values, and comparison of the calculated and experimental values for a set of 30 SHV-1/BLIP complexes yielded a correlation coefficient of 0.77. Structures of the two complexes with the highest affinity, SHV-1/BLIP (E73M) and SHV-1/BLIP (E73M, S130K, S146M), are presented at 1.7 A resolution. While the predicted structures have much in common with the experimentally determined structures, they do not coincide perfectly; in particular a salt bridge between SHV-1 D104 and BLIP K74 is observed in the experimental structures, but not in the predicted design conformations. This discrepancy highlights the difficulty of modeling salt bridge interactions with a protein design algorithm that approximates side chains as discrete rotamers. Nevertheless, while local structural features of the interface were sometimes miscalculated, EGAD is globally successful in designing complexes with increased affinity.
-'''Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) E73M/S130K/S146M complex'''
+Computational redesign of the SHV-1 beta-lactamase/beta-lactamase inhibitor protein interface.,Reynolds KA, Hanes MS, Thomson JM, Antczak AJ, Berger JM, Bonomo RA, Kirsch JF, Handel TM J Mol Biol. 2008 Oct 24;382(5):1265-75. Epub 2008 May 29. PMID:18775544<ref>PMID:18775544</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3c4o" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-C4O is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Klebsiella_pneumoniae Klebsiella pneumoniae] and [http://en.wikipedia.org/wiki/Streptomyces_clavuligerus Streptomyces clavuligerus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3C4O OCA].
+*[[Beta-lactamase 3D structures|Beta-lactamase 3D structures]]
-[[Category: Beta-lactamase]]
+*[[TEM1-beta-Lactamase/beta-lactamase Inhibitor Protein (BLIP)|TEM1-beta-Lactamase/beta-lactamase Inhibitor Protein (BLIP)]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Klebsiella pneumoniae]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
 [[Category: Streptomyces clavuligerus]]
-[[Category: Antczak, A J.]]
+[[Category: Antczak AJ]]
-[[Category: Berger, J M.]]
+[[Category: Berger JM]]
-[[Category: Bonomo, R A.]]
+[[Category: Bonomo RA]]
-[[Category: Handel, T M.]]
+[[Category: Handel TM]]
-[[Category: Hanes, M S.]]
+[[Category: Hanes MS]]
-[[Category: Kirsch, J F.]]
+[[Category: Kirsch JF]]
-[[Category: Reynolds, K A.]]
+[[Category: Reynolds KA]]
-[[Category: Thomson, J M.]]
+[[Category: Thomson JM]]
-[[Category: Antibiotic resistance]]
-[[Category: Beta-lactamase]]
-[[Category: Beta-lactamase inhibitory protein]]
-[[Category: Blip]]
-[[Category: Hydrolase]]
-[[Category: Hydrolase/hydrolase inhibitor complex]]
-[[Category: Plasmid]]
-[[Category: Protein-protein complex]]
-[[Category: Secreted]]
-[[Category: Shv-1]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed May 28 09:20:25 2008''