Scripps VIVO scripps research logo

  • Index
  • Log in
  • Home
  • People
  • Organizations
  • Research
  • Events
Search form
As of April 1st VIVO Scientific Profiles will no longer updated for faculty, and the link to VIVO will be removed from the library website. Faculty profile pages will continue to be updated via Interfolio. VIVO will continue being used behind the scenes to update graduate student profiles. Please contact helplib@scripps.edu if you have questions.
How to download citations from VIVO | Alternative profile options

Probing ligand recognition in the decarboxylase antibody 21d8: Implications for the catalytic mechanism

Academic Article
uri icon
  • Overview
  • Identity
  • Additional Document Info
  • View All
scroll to property group menus

Overview

related to degree

  • Hotta, Kinya, Ph.D. in Chemistry, Scripps Research 1996 - 2001

authors

  • Hotta, Kinya
  • Wilson, Ian
  • Hilvert, Donald M.

publication date

  • January 2002

journal

  • Biochemistry  Journal

abstract

  • Antibody 21D8, which was elicited with a naphthalene-1,5-disulfonate hapten, catalyzes the medium-sensitive decarboxylation of 5-nitro-3-carboxybenzisoxazole. Structural studies on the hapten-antibody complex show that the active site contains two anion binding pockets separated by a hydrophobic region. To gain further insight into the ligand binding and catalytic mechanism of 21D8, six site-directed mutants were prepared, four for investigating the role of each of the two hapten sulfonate binding sites and two for examining packing interactions between bound ligands and the binding pocket. With the exception of an Arg(L46)Met substitution in the more deeply buried sulfonate binding pocket, modification of the active site resulted in reductions in catalytic efficiency (k(cat)/k(uncat)), ranging between 3- and 23-fold. Importantly, and contrary to predictions based on computational docking experiments, the differential effects of the individual mutations on the K(m), K(TS), and K(product) parameters suggest that only substrate binding modes which place the carboxylate group in the more solvent-exposed sulfonate binding site are catalytically relevant. Such an orientation would permit a potentially significant interaction between the developing oxyanion in the transition state and the side chain of Arg(L96). Incomplete desolvation of the carboxylate in this orientation may also help explain the modest efficiency of 21D8 compared to the most accelerating aprotic dipolar organic solvents.

subject areas

  • Amino Acid Substitution
  • Antibodies, Catalytic
  • Base Sequence
  • Binding Sites
  • Catalysis
  • Haptens
  • Kinetics
  • Ligands
  • Models, Molecular
  • Mutagenesis, Site-Directed
  • Protein Conformation
  • Recombinant Proteins
scroll to property group menus

Identity

International Standard Serial Number (ISSN)

  • 0006-2960

Digital Object Identifier (DOI)

  • 10.1021/bi0158167

PubMed ID

  • 11790098
scroll to property group menus

Additional Document Info

start page

  • 772

end page

  • 779

volume

  • 41

issue

  • 3

©2022 The Scripps Research Institute | Terms of Use | Powered by VIVO

  • About
  • Contact Us
  • Support