2dqu

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{{STRUCTURE_2dqu| PDB=2dqu | SCENE= }}
{{STRUCTURE_2dqu| PDB=2dqu | SCENE= }}
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'''Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog'''
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===Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog===
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==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 17428500 is the PubMed ID number.
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{{ABSTRACT_PUBMED_17428500}}
==About this Structure==
==About this Structure==
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==Reference==
==Reference==
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:[http://www.ncbi.nlm.nih.gov/pubmed/17428500 17428500]
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:[http://www.ncbi.nlm.nih.gov/pubmed/17428500 17428500]
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Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: evidence for an essential histidine involved in transition state stabilization., Miyashita H, Hara T, Tanimura R, Fukuyama S, Cagnon C, Kohara A, Fujii I, J Mol Biol. 1997 Apr 18;267(5):1247-57. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9150409 9150409]
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A common ancestry for multiple catalytic antibodies generated against a single transition-state analog., Miyashita H, Hara T, Tamimura R, Tanaka F, Kikuchi M, Fujii I, Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10757. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/7938025 7938025]
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A common ancestry for multiple catalytic antibodies generated against a single transition-state analog., Miyashita H, Hara T, Tanimura R, Tanaka F, Kikuchi M, Fujii I, Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):6045-9. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8016113 8016113]
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Prodrug activation via catalytic antibodies., Miyashita H, Karaki Y, Kikuchi M, Fujii I, Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5337-40. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8506382 8506382]
[[Category: Fujii, I.]]
[[Category: Fujii, I.]]
[[Category: Ito, N.]]
[[Category: Ito, N.]]
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[[Category: Fab]]
[[Category: Fab]]
[[Category: Immunoglobulin]]
[[Category: Immunoglobulin]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 00:58:57 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 09:34:42 2008''

Revision as of 06:34, 29 July 2008

Image:2dqu.png

Template:STRUCTURE 2dqu

Crystal form II: high resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog

Template:ABSTRACT PUBMED 17428500

About this Structure

This structure supersedes the now removed PDB entry 1hyy. Full crystallographic information is available from OCA.

Reference

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

Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: evidence for an essential histidine involved in transition state stabilization., Miyashita H, Hara T, Tanimura R, Fukuyama S, Cagnon C, Kohara A, Fujii I, J Mol Biol. 1997 Apr 18;267(5):1247-57. PMID:9150409

A common ancestry for multiple catalytic antibodies generated against a single transition-state analog., Miyashita H, Hara T, Tamimura R, Tanaka F, Kikuchi M, Fujii I, Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10757. PMID:7938025

A common ancestry for multiple catalytic antibodies generated against a single transition-state analog., Miyashita H, Hara T, Tanimura R, Tanaka F, Kikuchi M, Fujii I, Proc Natl Acad Sci U S A. 1994 Jun 21;91(13):6045-9. PMID:8016113

Prodrug activation via catalytic antibodies., Miyashita H, Karaki Y, Kikuchi M, Fujii I, Proc Natl Acad Sci U S A. 1993 Jun 1;90(11):5337-40. PMID:8506382

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