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| - | ==FAB FRAGMENT OF PLP-DEPENDENT CATALYTIC ANTIBODY 15A9 IN COMPLEX WITH PHOSPHOPYRIDOXYL-D-ALANINE== | + | |
| - | <StructureSection load='2bmk' size='340' side='right' caption='[[2bmk]], [[Resolution|resolution]] 2.30Å' scene=''> | + | ==Fab fragment of PLP-dependent catalytic antibody 15A9 in complex with phosphopyridoxyl-D-alanine== |
| | + | <StructureSection load='2bmk' size='340' side='right'caption='[[2bmk]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2bmk]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2BMK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2BMK FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2bmk]] 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=2BMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2BMK FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wc7|1wc7]], [[1wcb|1wcb]]</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=PDD:N-(5-PHOSPHOPYRIDOXYL)-D-ALANINE'>PDD</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bmk OCA], [http://pdbe.org/2bmk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2bmk RCSB], [http://www.ebi.ac.uk/pdbsum/2bmk PDBsum]</span></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=2bmk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2bmk OCA], [https://pdbe.org/2bmk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2bmk RCSB], [https://www.ebi.ac.uk/pdbsum/2bmk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2bmk ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
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| | Check<jmol> | | Check<jmol> |
| | <jmolCheckbox> | | <jmolCheckbox> |
| - | <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/2bmk_consurf.spt"</scriptWhenChecked> | + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/bm/2bmk_consurf.spt"</scriptWhenChecked> |
| - | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> |
| | <text>to colour the structure by Evolutionary Conservation</text> | | <text>to colour the structure by Evolutionary Conservation</text> |
| | </jmolCheckbox> | | </jmolCheckbox> |
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| | | | |
| | ==See Also== | | ==See Also== |
| - | *[[Monoclonal Antibody|Monoclonal Antibody]] | + | *[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Lk3 transgenic mice]] | + | [[Category: Large Structures]] |
| - | [[Category: Christen, P]] | + | [[Category: Mus musculus]] |
| - | [[Category: Golinelli-Pimpaneau, B]] | + | [[Category: Christen P]] |
| - | [[Category: Catalytic antibody]] | + | [[Category: Golinelli-Pimpaneau B]] |
| - | [[Category: Hapten]]
| + | |
| - | [[Category: Immune system]]
| + | |
| - | [[Category: Phosphopyridoxyl-l-lysine]]
| + | |
| - | [[Category: Pyridoxal-phosphate]]
| + | |
| - | [[Category: Transamination]]
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| Structural highlights
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
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.
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Golinelli-Pimpaneau B, Luthi C, Christen P. Structural basis for D-amino acid transamination by the pyridoxal 5'-phosphate-dependent catalytic antibody 15A9. J Biol Chem. 2006 Aug 18;281(33):23969-77. Epub 2006 Jun 21. PMID:16790434 doi:10.1074/jbc.M602184200
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