1wcb: Difference between revisions

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-{{Seed}}
-[[Image:1wcb.png|left|200px]]
-<!--
+==PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN==
-The line below this paragraph, containing "STRUCTURE_1wcb", creates the "Structure Box" on the page.
+<StructureSection load='1wcb' size='340' side='right'caption='[[1wcb]], [[Resolution|resolution]] 2.50&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'>[[1wcb]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WCB 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]] 2.5&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PE1:N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE'>PE1</scene></td></tr>
-{{STRUCTURE_1wcb|  PDB=1wcb  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wcb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wcb OCA], [https://pdbe.org/1wcb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wcb RCSB], [https://www.ebi.ac.uk/pdbsum/1wcb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wcb ProSAT]</span></td></tr>
+</table>
+== 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/wc/1wcb_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=1wcb ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Antibody 15A9, raised with 5'-phosphopyridoxyl (PPL)-N(epsilon)-acetyl-L-lysine as hapten, catalyzes the reversible transamination of hydrophobic D-amino acids with pyridoxal 5'-phosphate (PLP). The crystal structures of the complexes of Fab 15A9 with PPL-L-alanine, PPL-D-alanine, and the hapten were determined at 2.3, 2.3, and 2.5A resolution, respectively, and served for modeling the complexes with the corresponding planar imine adducts. The conformation of the PLP-amino acid adduct and its interactions with 15A9 are similar to those occurring in PLP-dependent enzymes, except that the amino acid substrate is only weakly bound, and, due to the immunization and selection strategy, the lysine residue that covalently binds PLP in these enzymes is missing. However, the N-acetyl-L-lysine moiety of the hapten appears to have selected for aromatic residues in hypervariable loop H3 (Trp-H100e and Tyr-H100b), which, together with Lys-H96, create an anion-binding environment in the active site. The structural situation and mutagenesis experiments indicate that two catalytic residues facilitate the transamination reaction of the PLP-D-alanine aldimine. The space vacated by the absent L-lysine side chain of the hapten can be filled, in both PLP-alanine aldimine complexes, by mobile Tyr-H100b. This group can stabilize a hydroxide ion, which, however, abstracts the C alpha proton only from D-alanine. Together with the absence of any residue capable of deprotonating C alpha of L-alanine, Tyr-H100b thus underlies the enantiomeric selectivity of 15A9. The reprotonation of C4' of PLP, the rate-limiting step of 15A9-catalyzed transamination, is most likely performed by a water molecule that, assisted by Lys-H96, produces a hydroxide ion stabilized by the anion-binding environment.
-===PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH ITS HAPTEN===
+Structural basis for D-amino acid transamination by the pyridoxal 5'-phosphate-dependent catalytic antibody 15A9.,Golinelli-Pimpaneau B, Luthi C, Christen P J Biol Chem. 2006 Aug 18;281(33):23969-77. Epub 2006 Jun 21. PMID:16790434<ref>PMID:16790434</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1wcb" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_16790434}}, adds the Publication Abstract to the page
+*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 16790434 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_16790434}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-WCB is a 4 chains structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WCB OCA].
-==Reference==
-<ref group="xtra">PMID:16790434</ref><references group="xtra"/>
 [[Category: Mus musculus]]
-[[Category: Christen, P.]]
+[[Category: Christen P]]
-[[Category: Golinelli-Pimpaneau, B.]]
+[[Category: Golinelli-Pimpaneau B]]
-[[Category: Catalytic antibody]]
-[[Category: Hapten]]
-[[Category: Immune system]]
-[[Category: Phosphopyridoxyl-l-lysine]]
-[[Category: Pyridoxal-phosphate]]
-[[Category: Transamination]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 00:29:39 2009''