2wpb: Difference between revisions

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-{{Seed}}
-[[Image:2wpb.jpg|left|200px]]
-<!--
+==Crystal structure of the E192N mutant of E. Coli N-acetylneuraminic acid lyase in complex with pyruvate and the inhibitor (2R,3R)-2,3,4- trihydroxy-N,N-dipropylbutanamide in space group P21 crystal form I==
-The line below this paragraph, containing "STRUCTURE_2wpb", creates the "Structure Box" on the page.
+<StructureSection load='2wpb' size='340' side='right'caption='[[2wpb]], [[Resolution|resolution]] 2.05&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'>[[2wpb]] is a 4 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=2WPB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WPB 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]] 2.05&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KPI:(2S)-2-AMINO-6-[(1-HYDROXY-1-OXO-PROPAN-2-YLIDENE)AMINO]HEXANOIC+ACID'>KPI</scene>, <scene name='pdbligand=ZZI:(2R,3R)-2,3,4-TRIHYDROXY-N,N-DIPROPYLBUTANAMIDE'>ZZI</scene></td></tr>
-{{STRUCTURE_2wpb|  PDB=2wpb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2wpb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wpb OCA], [https://pdbe.org/2wpb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wpb RCSB], [https://www.ebi.ac.uk/pdbsum/2wpb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wpb ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/NANA_ECOLI NANA_ECOLI] Catalyzes the cleavage of N-acetylneuraminic acid (sialic acid) to form pyruvate and N-acetylmannosamine via a Schiff base intermediate.[HAMAP-Rule:MF_01237]
+== 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/wp/2wpb_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=2wpb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The substrate specificity of Escherichia coli N-acetylneuraminic acid lyase was previously switched from the natural condensation of pyruvate with N-acetylmannosamine, yielding N-acetylneuraminic acid, to aldol condensation, generating N-alkylcarboxamide analogues of N-acetylneuraminic acid. This was achieved by a single mutation of Glu192 to Asn. In order to analyze the structural changes involved and to more fully understand the basis of this switch in specificity, we have isolated all 20 variants of the enzyme at position 192 and determined the activities with a range of substrates. We have also determined five high-resolution crystal structures: the structures of wild-type E. coli N-acetylneuraminic acid lyase in the presence and in the absence of pyruvate, the structures of the E192N variant in the presence and in the absence of pyruvate, and the structure of the E192N variant in the presence of pyruvate and a competitive inhibitor (2R,3R)-2,3,4-trihydroxy-N,N-dipropylbutanamide. All structures were solved in space group P2(1) at resolutions ranging from 1.65 A to 2.2 A. A comparison of these structures, in combination with the specificity profiles of the variants, reveals subtle differences that explain the details of the specificity changes. This work demonstrates the subtleties of enzyme-substrate interactions and the importance of determining the structures of enzymes produced by directed evolution, where the specificity determinants may change from one substrate to another.
-===CRYSTAL STRUCTURE OF THE E192N MUTANT OF E. COLI N-ACETYLNEURAMINIC ACID LYASE IN COMPLEX WITH PYRUVATE AND THE INHIBITOR (2R,3R)-2,3,4-TRIHYDROXY-N,N-DIPROPYLBUTANAMIDE IN SPACE GROUP P21 CRYSTAL FORM I===
+Structural Insights into Substrate Specificity in Variants of N-Acetylneuraminic Acid Lyase Produced by Directed Evolution.,Campeotto I, Bolt AH, Harman TA, Dennis C, Trinh CH, Phillips SE, Nelson A, Pearson AR, Berry A J Mol Biol. 2010 Sep 6. PMID:20826162<ref>PMID:20826162</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2wpb" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-WPB is a 4 chains structure with sequences 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=2WPB OCA].
+*[[N-acetylneuraminate lyase 3D structures|N-acetylneuraminate lyase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Escherichia coli]]
-[[Category: N-acetylneuraminate lyase]]
+[[Category: Large Structures]]
-[[Category: Berry, A.]]
+[[Category: Berry A]]
-[[Category: Bolt, A H.]]
+[[Category: Bolt AH]]
-[[Category: Campeotto, I.]]
+[[Category: Campeotto I]]
-[[Category: Dennis, C A.]]
+[[Category: Dennis CA]]
-[[Category: Harman, T A.]]
+[[Category: Harman TA]]
-[[Category: Nelson, A.]]
+[[Category: Nelson A]]
-[[Category: Pearson, A R.]]
+[[Category: Pearson AR]]
-[[Category: Phillips, S E.V.]]
+[[Category: Phillips SEV]]
-[[Category: Trinh, C H.]]
+[[Category: Trinh CH]]
-[[Category: Aldolase]]
-[[Category: Carbohydrate metabolism]]
-[[Category: Lyase]]
-[[Category: Protein engineering]]
-[[Category: Schiff base]]
-[[Category: Substrate specificity]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:50:08 2010''