1ND0

CATIONIC CYCLIZATION ANTIBODY 4C6 COMPLEX WITH TRANSITION STATE ANALOG

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 

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Literature

Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction

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

(2003) J Mol Biol 329: 69-83

  • DOI: 10.1016/s0022-2836(03)00406-6
  • Primary Citation of Related Structures:  
    1NCW, 1ND0

  • PubMed 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 ...

    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.

    Organizational Affiliation: 

    Department of Molecular Biology BBC206, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN IGG2AA, C, E, G219Mus musculusMutation(s): 0 
Gene Names: Igk
UniProt
Find proteins for Q58EU8 (Mus musculus)
Explore Q58EU8 
Go to UniProtKB:  Q58EU8
Entity Groups  
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UniProt GroupQ58EU8
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN IGG2AB, D, F, H222Mus musculusMutation(s): 0 
Gene Names: Igh-1a
UniProt
Find proteins for P01865 (Mus musculus)
Explore P01865 
Go to UniProtKB:  P01865
Entity Groups  
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UniProt GroupP01865
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.242 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.572α = 75.51
b = 95.164β = 88.64
c = 141.058γ = 89.28
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data reduction
AMoREphasing
CNSrefinement
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2002-12-05 
  • Released Date: 2003-05-13 
    • Deposition Author(s): Zhu, X., Wilson, I.A.

Revision History  (Full details and data files)

  • Version 1.0: 2003-05-13
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance