3b8u: Difference between revisions

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-{{Seed}}
-[[Image:3b8u.jpg|left|200px]]
-<!--
+==Crystal structure of Escherichia coli alaine racemase mutant E221A==
-The line below this paragraph, containing "STRUCTURE_3b8u", creates the "Structure Box" on the page.
+<StructureSection load='3b8u' size='340' side='right'caption='[[3b8u]], [[Resolution|resolution]] 3.00&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'>[[3b8u]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli_K-12 Escherichia coli K-12]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3B8U OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3B8U 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]] 3&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=KCX:LYSINE+NZ-CARBOXYLIC+ACID'>KCX</scene>, <scene name='pdbligand=PLP:PYRIDOXAL-5-PHOSPHATE'>PLP</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-{{STRUCTURE_3b8u|  PDB=3b8u  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3b8u FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3b8u OCA], [https://pdbe.org/3b8u PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3b8u RCSB], [https://www.ebi.ac.uk/pdbsum/3b8u PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3b8u ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ALR1_ECOLI ALR1_ECOLI] Catalyzes the interconversion of L-alanine and D-alanine. Provides the D-alanine required for cell wall biosynthesis.<ref>PMID:18434499</ref>
+== 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/b8/3b8u_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=3b8u ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Alanine racemase (Alr) is an important enzyme that catalyzes the interconversion of L-alanine and D-alanine, an essential building block in the peptidoglycan biosynthesis. For the small size of the Alr active site, its conserved substrate entryway has been proposed as a potential choice for drug design. In this work, we fully analyzed the crystal structures of the native, the D-cycloserine-bound, and four mutants (P219A, E221A, E221K, and E221P) of biosynthetic Alr from Escherichia coli (EcAlr) and studied the potential roles in substrate orientation for the key residues involved in the substrate entryway in conjunction with the enzymatic assays. Structurally, it was discovered that EcAlr is similar to the Pseudomonas aeruginosa catabolic Alr in both overall and active site geometries. Mutation of the conserved negatively charged residue aspartate 164 or glutamate 165 at the substrate entryway could obviously reduce the binding affinity of enzyme against the substrate and decrease the turnover numbers in both D- to L-Ala and L- to D-Ala directions, especially when mutated to lysine with the opposite charge. However, mutation of Pro219 or Glu221 had only negligible or a small influence on the enzymatic activity. Together with the enzymatic and structural investigation results, we thus proposed that the negatively charged residues Asp164 and Glu165 around the substrate entryway play an important role in substrate orientation with cooperation of the positively charged Arg280 and Arg300 on the opposite monomer. Our findings are expected to provide some useful structural information for inhibitor design targeting the substrate entryway of Alr.
-===Crystal structure of Escherichia coli alaine racemase mutant E221A===
+Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis.,Wu D, Hu T, Zhang L, Chen J, Du J, Ding J, Jiang H, Shen X Protein Sci. 2008 Jun;17(6):1066-76. Epub 2008 Apr 23. PMID:18434499<ref>PMID:18434499</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3b8u" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_18434499}}, adds the Publication Abstract to the page
+*[[Alanine racemase 3D structures|Alanine racemase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 18434499 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_18434499}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Escherichia coli K-12]]
-B8U 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=3B8U OCA].
+[[Category: Large Structures]]
+[[Category: Hu T]]
-==Reference==
+[[Category: Jiang H]]
-Residues Asp164 and Glu165 at the substrate entryway function potently in substrate orientation of alanine racemase from E. coli: Enzymatic characterization with crystal structure analysis., Wu D, Hu T, Zhang L, Chen J, Du J, Ding J, Jiang H, Shen X, Protein Sci. 2008 Jun;17(6):1066-76. Epub 2008 Apr 23. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18434499 18434499]
+[[Category: Shen X]]
-[[Category: Alanine racemase]]
+[[Category: Wu D]]
-[[Category: Escherichia coli]]
+[[Category: Zhang L]]
-[[Category: Single protein]]
-[[Category: Hu, T.]]
-[[Category: Jiang, H.]]
-[[Category: Shen, X.]]
-[[Category: Wu, D.]]
-[[Category: Zhang, L.]]
-[[Category: Alpha/beta barrel]]
-[[Category: Cell shape]]
-[[Category: Cell wall biogenesis/degradation]]
-[[Category: Isomerase]]
-[[Category: Peptidoglycan synthesis]]
-[[Category: Pyridoxal phosphate]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul  9 10:31:22 2008''