PDBsum entry: 3cfj

Immune system

PDB-id: 3cfj

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References

PROCHECK

Protein chains

215 a.a. *

224 a.a. *

Ligands

GOL ×3

SO4 ×3

Waters ×518

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

3cfj

Name:

Immune system

Title:

Crystal structure of catalytic elimination antibody 34e4, orthorhombic crystal form

Structure:

Catalytic antibody fab 34e4 light chain. Chain: l, a, c, e. Engineered: yes. Other_details: fusion protein of the variable domain (author residues 1-105) and the constant domain (unp residues 131-239). Catalytic antibody fab 34e4 heavy chain. Chain: h, b, d, f. Engineered: yes.

Source:

Mus musculus, homo sapiens. Mouse, human. Gene: catalytic antibody fab 34e4 light chain. Expressed in: escherichia coli.

UniProt:

Chains L, A, C, E: Q8TCD0 (Q8TCD0_HUMAN)

Seq:	239 a.a.
Struc:	215 a.a.*

Chains H, B, D, F: A8K008 (A8K008_HUMAN)

Seq:

Struc:

Seq:

472 a.a.

Struc:

224 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 114 residue positions (black crosses)

Resolution:

2.60Å

R-factor:

0.202

R-free:

0.253

Authors:

E.W.Debler,I.A.Wilson

Key ref:

E.W.Debler et al. (2008). Conformational isomerism can limit antibody catalysis.. J Biol Chem, 283, 16554-16560. [PubMed id: 18417480] [DOI: 10.1074/jbc.M710256200]

Date:

04-Mar-08

Release date:

15-Apr-08

Related entries:

1y0l
the crystal structure of catalytic antibody 34e4 in complex
with hapten, determined at 2.50 angstrom resolution
1y18
the crystal structure of catalytic antibody 34e4 e(h50)d
mutant in complex with hapten, determined at 2.80 angstrom
resolution
3cfk
crystal structure of catalytic elimination antibody 34e4,
triclinic crystal form

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Surface

Key reference

DOI no: 10.1074/jbc.M710256200

J Biol Chem 283:16554-16560 (2008)

PubMed id: 18417480

Conformational isomerism can limit antibody catalysis.

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

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 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.

Selected figure(s)

Figure 2.
FIGURE 2. Antibody combining site of 34E4 in its unliganded state. The heavy and light chains are colored in blue and green, respectively. The 2F[o] - 1F[c] [A]-weighted electron density maps are contoured at 1.1 . Antibody 34E4 predominantly exists in the displayed closed conformation, where Trp^L91 swings into the binding pocket, occluding the active site. The electron density of Trp^L91 is less well defined than surrounding residues, indicating increased flexibility and/or multiple conformations.

Figure 4.
FIGURE 4. Molecular surface representation of free (A) and hapten-bound (B) 34E4. The hapten is displayed as pink stick model. The architecture of the antibody combining site is dramatically different in the two states. The shallow indentation of the predominant closed conformation of the antibody in the unliganded form (A) can convert to an open conformation that can then harbor the hapten in a deep cavity (B).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2008, 283, 16554-16560) copyright 2008.

Figures were selected by the author.