43ca: Difference between revisions

Revision as of 20:12, 21 February 2008

CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9 ANTIBODY WITH BOUND P-NITROPHENOL

OverviewOverview

Among catalytic antibodies, the well-characterized antibody 43C9 is unique in its ability to catalyze the difficult, but desirable, reaction of selective amide hydrolysis. The crystallographic structures that we present here for the single-chain variable fragment of the 43C9 antibody, both with and without the bound product p -nitrophenol, strongly support and extend the structural and mechanistic information previously provided by a three-dimensional computational model, together with extensive biochemical, kinetics, and mutagenesis results. The structures reveal an unexpected extended beta-sheet conformation of the third complementarity determining region of the heavy chain, which may be coupled to the novel indole ring orientation of the adjacent Trp H103. This unusual conformation creates an antigen-binding site that is significantly deeper than predicted in the computational model, with a hydrophobic pocket that encloses the p -nitrophenol product. Despite these differences, the previously proposed roles for Arg L96 in transition-state stabilization and for His L91 as the nucleophile that forms a covalent acyl-antibody intermediate are fully supported by the crystallographic structures. His L91 is now centered at the bottom of the antigen-binding site with the imidazole ring poised for nucleophilic attack. His L91, Arg L96, and the bound p -nitrophenol are linked into a hydrogen-bonding network by two well-ordered water molecules. These water molecules may mimic the positions of the phosphonamidate oxygen atoms of the antigen, which in turn mimic the transition state of the reaction. This network also contains His H35, suggesting that this residue may also stabilize the transition-states. A possible proton-transfer pathway from His L91 through two tyrosine residues may assist nucleophilic attack. Although transition-state stabilization is commonly observed in esterolytic antibodies, nucleophilic attack appears to be unique to 43C9 and accounts for the unusually high catalytic activity of this antibody.

About this StructureAbout this Structure

43CA is a Protein complex structure of sequences from Mus musculus with as ligand. Full crystallographic information is available from OCA.

ReferenceReference

Structural basis for amide hydrolysis catalyzed by the 43C9 antibody., Thayer MM, Olender EH, Arvai AS, Koike CK, Canestrelli IL, Stewart JD, Benkovic SJ, Getzoff ED, Roberts VA, J Mol Biol. 1999 Aug 13;291(2):329-45. PMID:10438624

Page seeded by OCA on Thu Feb 21 19:12:14 2008

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-[[Image:43ca.gif|left|200px]]<br />
+[[Image:43ca.gif|left|200px]]<br /><applet load="43ca" size="350" color="white" frame="true" align="right" spinBox="true"
-<applet load="43ca" size="450" color="white" frame="true" align="right" spinBox="true"
 caption="43ca, resolution 2.300&Aring;" />
 '''CRYSTALLOGRAPHIC STRUCTURE OF THE ESTEROLYTIC AND AMIDOLYTIC 43C9 ANTIBODY WITH BOUND P-NITROPHENOL'''<br />
 ==Overview==
-Among catalytic antibodies, the well-characterized antibody 43C9 is unique, in its ability to catalyze the difficult, but desirable, reaction of, selective amide hydrolysis. The crystallographic structures that we, present here for the single-chain variable fragment of the 43C9 antibody, both with and without the bound product p -nitrophenol, strongly support, and extend the structural and mechanistic information previously provided, by a three-dimensional computational model, together with extensive, biochemical, kinetics, and mutagenesis results. The structures reveal an, unexpected extended beta-sheet conformation of the third complementarity, determining region of the heavy chain, which may be coupled to the novel, indole ring orientation of the adjacent Trp H103. This unusual, conformation creates an antigen-binding site that is significantly deeper, than predicted in the computational model, with a hydrophobic pocket that, encloses the p -nitrophenol product. Despite these differences, the, previously proposed roles for Arg L96 in transition-state stabilization, and for His L91 as the nucleophile that forms a covalent acyl-antibody, intermediate are fully supported by the crystallographic structures. His, L91 is now centered at the bottom of the antigen-binding site with the, imidazole ring poised for nucleophilic attack. His L91, Arg L96, and the, bound p -nitrophenol are linked into a hydrogen-bonding network by two, well-ordered water molecules. These water molecules may mimic the, positions of the phosphonamidate oxygen atoms of the antigen, which in, turn mimic the transition state of the reaction. This network also, contains His H35, suggesting that this residue may also stabilize the, transition-states. A possible proton-transfer pathway from His L91 through, two tyrosine residues may assist nucleophilic attack. Although, transition-state stabilization is commonly observed in esterolytic, antibodies, nucleophilic attack appears to be unique to 43C9 and accounts, for the unusually high catalytic activity of this antibody.
+Among catalytic antibodies, the well-characterized antibody 43C9 is unique in its ability to catalyze the difficult, but desirable, reaction of selective amide hydrolysis. The crystallographic structures that we present here for the single-chain variable fragment of the 43C9 antibody, both with and without the bound product p -nitrophenol, strongly support and extend the structural and mechanistic information previously provided by a three-dimensional computational model, together with extensive biochemical, kinetics, and mutagenesis results. The structures reveal an unexpected extended beta-sheet conformation of the third complementarity determining region of the heavy chain, which may be coupled to the novel indole ring orientation of the adjacent Trp H103. This unusual conformation creates an antigen-binding site that is significantly deeper than predicted in the computational model, with a hydrophobic pocket that encloses the p -nitrophenol product. Despite these differences, the previously proposed roles for Arg L96 in transition-state stabilization and for His L91 as the nucleophile that forms a covalent acyl-antibody intermediate are fully supported by the crystallographic structures. His L91 is now centered at the bottom of the antigen-binding site with the imidazole ring poised for nucleophilic attack. His L91, Arg L96, and the bound p -nitrophenol are linked into a hydrogen-bonding network by two well-ordered water molecules. These water molecules may mimic the positions of the phosphonamidate oxygen atoms of the antigen, which in turn mimic the transition state of the reaction. This network also contains His H35, suggesting that this residue may also stabilize the transition-states. A possible proton-transfer pathway from His L91 through two tyrosine residues may assist nucleophilic attack. Although transition-state stabilization is commonly observed in esterolytic antibodies, nucleophilic attack appears to be unique to 43C9 and accounts for the unusually high catalytic activity of this antibody.
 ==About this Structure==
-CA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with NPO as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=43CA OCA].
+CA is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with <scene name='pdbligand=NPO:'>NPO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=43CA OCA].
 ==Reference==
@@ Line 14: / Line 13: @@
 [[Category: Mus musculus]]
 [[Category: Protein complex]]
-[[Category: Getzoff, E.D.]]
+[[Category: Getzoff, E D.]]
-[[Category: Roberts, V.A.]]
+[[Category: Roberts, V A.]]
-[[Category: Thayer, M.M.]]
+[[Category: Thayer, M M.]]
 [[Category: NPO]]
 [[Category: catalytic antibody]]
 [[Category: immunoglobulin]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:53:33 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 19:12:14 2008''