PDBsum entry 1ncw

Immune system

PDB id: 1ncw

Contents

Protein chains

219 a.a. *

222 a.a. *

Ligands

BEZ

GOL ×4

Waters ×577

* Residue conservation analysis

PDB id:

1ncw

Name:

Immune system

Title:

Cationic cyclization antibody 4c6 in complex with benzoic acid

Structure:

Immunoglobulin igg2a. Chain: l. Fragment: antibody fab fragment 4c6, light chain. Immunoglobulin igg2a. Chain: h. Fragment: antibody fab fragment 4c6, heavy chain

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Strain: 129g1x+. Other_details: purified from ascitic fluid. Other_details: purified from ascitic fluid

Biol. unit:

Dimer (from PQS)

Resolution:

1.30Å R-factor: 0.158 R-free: 0.208

Authors:

X.Zhu,I.A.Wilson

Key ref:

X.Zhu et al. (2003). Structural basis for antibody catalysis of a cationic cyclization reaction. J Mol Biol, 329, 69-83. PubMed id: 12742019 DOI: 10.1016/S0022-2836(03)00406-6

Date:

05-Dec-02 Release date: 13-May-03

Protein chain

Q58EU8  (Q58EU8_MOUSE) -  Igk protein from Mus musculus

Seq: 239 a.a.

Struc: 219 a.a.*

Protein chain

P01865  (GCAM_MOUSE) -  Immunoglobulin heavy constant gamma 2A from Mus musculus

Seq: 398 a.a.

Struc: 222 a.a.

* PDB and UniProt seqs differ at 14 residue positions (black crosses)

DOI no: 10.1016/S0022-2836(03)00406-6

J Mol Biol 329:69-83 (2003)

PubMed id: 12742019

Structural basis for antibody catalysis of a cationic cyclization reaction.

X.Zhu, A.Heine, F.Monnat, K.N.Houk, K.D.Janda, I.A.Wilson.

ABSTRACT

Antibody 4C6 efficiently catalyzes a cationic cyclization reaction. Crystal structures of the antibody 4C6 Fab in complex with benzoic acid and in complex with its eliciting hapten were determined to 1.30A and 2.45A resolution, respectively. These crystal structures, together with computational analysis, have elucidated a possible mechanism for the monocyclization reaction. The hapten complex revealed a combining site pocket with high shape complementarity to the hapten. This active site cleft is dominated by aromatic residues that shield the highly reactive carbocation intermediates from solvent and stabilize the carbocation intermediates through cation-pi interactions. Modeling of an acyclic olefinic sulfonate ester substrate and the transition state (TS) structures shows that the chair-like transition state is favored, and trapping by water directly produces trans-2-(dimethylphenylsilyl)-cyclohexanol, whereas the less favored boat-like transition state leads to cyclohexene. The only significant change observed upon hapten binding is a side-chain rotation of Trp(L89), which reorients to form the base of the combining site. Intriguingly, a benzoic acid molecule was sequestered in the combining site of the unliganded antibody. The 4C6 active site was compared to that observed in a previously reported tandem cyclization antibody 19A4 hapten complex. These cationic cyclization antibodies exhibit convergent structural features with terpenoid cyclases that appear to be important for catalysis.

Selected figure(s)

Figure 3.
Figure 3. Shape complementarity of benzoic acid (a) and hapten (b) in the antibody 4C6 combining site. The Fab 4C6-binding pockets are shown with the molecular surfaces (1.4 Å probe radius). The shape of active sites differs dramatically between two structures primarily due to the side-chain of TrpL89, which flips downward to form the base of the hapten-binding pocket by the rotation of the x[2] angle about 65° on hapten binding. For further information, see the text and Figure 4. The Figure was generated in GRASP. [59.]

Figure 9.
Figure 9. Docking of reactants (13, 15, 17) and TS structures (14, 16, 18) into the hapten-binding site of the 4C6 Fab structure. (a) Pathway yielding of (1S),(2S)-product, E[docked] (13)= -14.1 kcal/mol, E[docked] (14)= -10.6 kcal/mol. (b) Pathway yielding of the (1R),(2R)-enantiomeric product with E[docked] (15)= -14.7 kcal/mol and E[docked] (16)= -10.9 kcal/mol. (c) Pathway yielding cyclohexene, E[docked] (17)= -14.6 kcal/mol and E[docked] (18)= -9.2 kcal/mol. The first two TS, 14 and 16, correspond to both enantiomers of the chair-like TS, whereas the last one (18) is the boat-like TS.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 329, 69-83) copyright 2003.

Figures were selected by an automated process.