3CFK

Crystal structure of catalytic elimination antibody 34E4, triclinic crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Conformational isomerism can limit antibody catalysis.

Debler, E.W.Muller, R.Hilvert, D.Wilson, I.A.

(2008) J.Biol.Chem. 283: 16554-16560

  • DOI: 10.1074/jbc.M710256200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ligand binding to enzymes and antibodies is often accompanied by protein conformational changes. Although such structural adjustments may be conducive to enzyme catalysis, much less is known about their effect on reactions promoted by engineered cata ...

    Ligand binding to enzymes and antibodies is often accompanied by protein conformational changes. Although such structural adjustments may be conducive to enzyme catalysis, much less is known about their effect on reactions promoted by engineered catalytic antibodies. Crystallographic and pre-steady state kinetic analyses of antibody 34E4, which efficiently promotes the conversion of benzisoxazoles to salicylonitriles, show that the resting catalyst adopts two interconverting active-site conformations, only one of which is competent to bind substrate. In the predominant isomer, the indole side chain of Trp(L91) occupies the binding site and blocks ligand access. Slow conformational isomerization of this residue, on the same time scale as catalytic turnover, creates a deep and narrow binding site that can accommodate substrate and promote proton transfer using Glu(H50) as a carboxylate base. Although 34E4 is among the best catalysts for the deprotonation of benzisoxazoles, its efficiency appears to be significantly limited by this conformational plasticity of its active site. Future efforts to improve this antibody might profitably focus on stabilizing the active conformation of the catalyst. Analogous strategies may also be relevant to other engineered proteins that are limited by an unfavorable conformational pre-equilibrium.


    Organizational Affiliation

    Department of Molecular Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CATALYTIC ANTIBODY FAB 34E4 LIGHT CHAIN,Uncharacterized protein
L, A, C, E, G, J, M, O
216Homo sapiensMutation(s): 0 
Find proteins for Q8TCD0 (Homo sapiens)
Go to UniProtKB:  Q8TCD0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CATALYTIC ANTIBODY FAB 34E4 HEAVY CHAIN,Uncharacterized protein
H, B, D, F, I, K, N, P
227Homo sapiensMutation(s): 1 
Gene Names: DKFZp686P15220
Find proteins for Q6N089 (Homo sapiens)
Go to UniProtKB:  Q6N089
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
B3P
Query on B3P

Download SDF File 
Download CCD File 
M, O
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C11 H26 N2 O6
HHKZCCWKTZRCCL-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, E
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B, C, D, E, G, J, K, L, M, O
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.221 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 81.069α = 89.89
b = 106.299β = 90.04
c = 116.109γ = 89.48
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-04-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-07-19
    Type: Database references, Source and taxonomy, Structure summary