2g2u: Difference between revisions

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-{{Seed}}
-[[Image:2g2u.png|left|200px]]
-<!--
+==Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex==
-The line below this paragraph, containing "STRUCTURE_2g2u", creates the "Structure Box" on the page.
+<StructureSection load='2g2u' size='340' side='right'caption='[[2g2u]], [[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'>[[2g2u]] 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=2G2U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2G2U 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=2g2u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2g2u OCA], [https://pdbe.org/2g2u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2g2u RCSB], [https://www.ebi.ac.uk/pdbsum/2g2u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2g2u ProSAT]</span></td></tr>
-{{STRUCTURE_2g2u|  PDB=2g2u  |  SCENE=  }}
+</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/g2/2g2u_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=2g2u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Beta-lactamase inhibitor protein (BLIP) binds a variety of class A beta-lactamases with affinities ranging from micromolar to picomolar. Whereas the TEM-1 and SHV-1 beta-lactamases are almost structurally identical, BLIP binds TEM-1 approximately 1000-fold tighter than SHV-1. Determining the underlying source of this affinity difference is important for understanding the molecular basis of beta-lactamase inhibition and mechanisms of protein-protein interface specificity and affinity. Here we present the 1.6A resolution crystal structure of SHV-1.BLIP. In addition, a point mutation was identified, SHV D104E, that increases SHV.BLIP binding affinity from micromolar to nanomolar. Comparison of the SHV-1.BLIP structure with the published TEM-1.BLIP structure suggests that the increased volume of Glu-104 stabilizes a key binding loop in the interface. Solution of the 1.8A SHV D104K.BLIP crystal structure identifies a novel conformation in which this binding loop is removed from the interface. Using these structural data, we evaluated the ability of EGAD, a program developed for computational protein design, to calculate changes in the stability of mutant beta-lactamase.BLIP complexes. Changes in binding affinity were calculated within an error of 1.6 kcal/mol of the experimental values for 112 mutations at the TEM-1.BLIP interface and within an error of 2.2 kcal/mol for 24 mutations at the SHV-1.BLIP interface. The reasonable success of EGAD in predicting changes in interface stability is a promising step toward understanding the stability of the beta-lactamase.BLIP complexes and computationally assisted design of tight binding BLIP variants.
-===Crystal Structure of the SHV-1 Beta-lactamase/Beta-lactamase inhibitor protein (BLIP) complex===
+Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface.,Reynolds KA, Thomson JM, Corbett KD, Bethel CR, Berger JM, Kirsch JF, Bonomo RA, Handel TM J Biol Chem. 2006 Sep 8;281(36):26745-53. Epub 2006 Jun 29. PMID:16809340<ref>PMID:16809340</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2g2u" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16809340}}, 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 16809340 is the PubMed ID number.
+*[[TEM1-beta-Lactamase/beta-lactamase Inhibitor Protein (BLIP)|TEM1-beta-Lactamase/beta-lactamase Inhibitor Protein (BLIP)]]
--->
+== References ==
-{{ABSTRACT_PUBMED_16809340}}
+<references/>
+__TOC__
-==About this Structure==
+</StructureSection>
-G2U 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=2G2U OCA].
-==Reference==
-Structural and computational characterization of the SHV-1 beta-lactamase-beta-lactamase inhibitor protein interface., Reynolds KA, Thomson JM, Corbett KD, Bethel CR, Berger JM, Kirsch JF, Bonomo RA, Handel TM, J Biol Chem. 2006 Sep 8;281(36):26745-53. Epub 2006 Jun 29. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/16809340 16809340]
-[[Category: Beta-lactamase]]
 [[Category: Klebsiella pneumoniae]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
 [[Category: Streptomyces clavuligerus]]
-[[Category: Berger, J M.]]
+[[Category: Berger JM]]
-[[Category: Bethel, C R.]]
+[[Category: Bethel CR]]
-[[Category: Bonomo, R A.]]
+[[Category: Bonomo RA]]
-[[Category: Corbett, K D.]]
+[[Category: Corbett KD]]
-[[Category: Handel, T M.]]
+[[Category: Handel TM]]
-[[Category: Kirsch, J F.]]
+[[Category: Kirsch JF]]
-[[Category: Reynolds, K A.]]
+[[Category: Reynolds KA]]
-[[Category: Thomson, J M.]]
+[[Category: Thomson JM]]
-[[Category: Beta-lactamase]]
-[[Category: Beta-lactamase inhibitor]]
-[[Category: Blip]]
-[[Category: Protein-protein complex]]
-[[Category: Shv-1]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 03:11:49 2008''