2dqt: Difference between revisions
New page: left|200px<br /> <applet load="2dqt" size="450" color="white" frame="true" align="right" spinBox="true" caption="2dqt, resolution 1.80Å" /> '''High resolution cry... |
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[[Image:2dqt.gif|left|200px]]<br /> | [[Image:2dqt.gif|left|200px]]<br /><applet load="2dqt" size="350" color="white" frame="true" align="right" spinBox="true" | ||
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'''High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog'''<br /> | '''High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog'''<br /> | ||
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==About this Structure== | ==About this Structure== | ||
2DQT 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 CPD as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1HYX. Full crystallographic information is available from [http:// | 2DQT 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=CPD:'>CPD</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. This structure superseeds the now removed PDB entry 1HYX. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2DQT OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: immunoglobulin]] | [[Category: immunoglobulin]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jan 23 15:02:54 2008'' | ||
Revision as of 16:02, 23 January 2008
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High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog
OverviewOverview
Catalytic antibodies 6D9 and 9C10, which were induced by immunization with, a haptenic transition-state analog (TSA), catalyze the hydrolysis of a, nonbioactive chloramphenicol monoester derivative to generate a bioactive, chloramphenicol. These antibodies stabilize the transition state to, catalyze the hydrolysis reaction, strictly according to the theoretical, relationship: for 6D9, k(cat)/k(uncat)=895 and K(S)/K(TSA)=900, and for, 9C10, k(cat)/k(uncat)=56 and K(S)/K(TSA)=60. To elucidate the molecular, basis of the antibody-catalyzed reaction, the crystal structure of 6D9 was, determined, and the binding thermodynamics of 6D9 and 9C10 with both the, substrate and the TSA were analyzed using isothermal titration, calorimetry. The crystal structure of the unliganded 6D9 Fab was, determined at 2.25 A resolution and compared with that of the TSA-liganded, 6D9 Fab reported previously, showing that the TSA is bound into the, hydrophobic pocket of the antigen-combining site in an "induced fit", manner, especially at the L1 and H3 CDR loops. Thermodynamic analyses, showed that 6D9 binds the substrate of the TSA with a positive DeltaS, differing from general thermodynamic characteristics of antigen-antibody, interactions. This positive DeltaS could be due to the hydrophobic, interactions between 6D9 and the substrate or the TSA mediated by Trp, H100i. The difference in DeltaG between substrate and TSA-binding to 6D9, was larger than that to 9C10, which is in good correlation with the larger, k(cat) value of 6D9. Interestingly, the DeltaDeltaG was mainly because of, the DeltaDeltaH. The correlation between k(cat) and DeltaDeltaH is, suggestive of "enthalpic strain" leading to destabilization of, antibody-substrate complexes. Together with X-ray structural analyses, the, thermodynamic analyses suggest that upon binding the substrate, the, antibody alters the conformation of the ester moiety in the substrate from, the planar Z form to a thermodynamically unstable twisted conformation, followed by conversion into the transition state. Enthalpic strain also, contributes to the transition-state stabilization by destabilizing the, ground state, and its degree is much larger for the more efficient, catalytic antibody, 6D9.
About this StructureAbout this Structure
2DQT is a Protein complex structure of sequences from Mus musculus with as ligand. This structure superseeds the now removed PDB entry 1HYX. Full crystallographic information is available from OCA.
ReferenceReference
Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis., Oda M, Ito N, Tsumuraya T, Suzuki K, Sakakura M, Fujii I, J Mol Biol. 2007 May 25;369(1):198-209. Epub 2007 Mar 15. PMID:17428500
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