2DQT

High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and a transition-state analog


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Thermodynamic and structural basis for transition-state stabilization in antibody-catalyzed hydrolysis

Oda, M.Ito, N.Tsumuraya, T.Suzuki, K.Sakakura, M.Fujii, I.

(2007) J Mol Biol 369: 198-209

  • DOI: https://doi.org/10.1016/j.jmb.2007.03.023
  • Primary Citation of Related Structures:  
    2DQT, 2DQU, 2DTM

  • PubMed Abstract: 

    Catalytic antibodies 6D9 and 9C10, which were induced by immunization with a haptenic transition-state analog (TSA), catalyze the hydrolysis of a nonbioactive chloramphenicol monoester derivative to generate a bioactive chloramphenicol. These antibodies stabilize the transition state to catalyze the hydrolysis reaction, strictly according to the theoretical relationship: for 6D9, k(cat)/k(uncat)=895 and K(S)/K(TSA)=900, and for 9C10, k(cat)/k(uncat)=56 and K(S)/K(TSA)=60. To elucidate the molecular basis of the antibody-catalyzed reaction, the crystal structure of 6D9 was determined, and the binding thermodynamics of 6D9 and 9C10 with both the substrate and the TSA were analyzed using isothermal titration calorimetry. The crystal structure of the unliganded 6D9 Fab was determined at 2.25 A resolution and compared with that of the TSA-liganded 6D9 Fab reported previously, showing that the TSA is bound into the hydrophobic pocket of the antigen-combining site in an "induced fit" manner, especially at the L1 and H3 CDR loops. Thermodynamic analyses showed that 6D9 binds the substrate of the TSA with a positive DeltaS, differing from general thermodynamic characteristics of antigen-antibody interactions. This positive DeltaS could be due to the hydrophobic interactions between 6D9 and the substrate or the TSA mediated by Trp H100i. The difference in DeltaG between substrate and TSA-binding to 6D9 was larger than that to 9C10, which is in good correlation with the larger k(cat) value of 6D9. Interestingly, the DeltaDeltaG was mainly because of the DeltaDeltaH. The correlation between k(cat) and DeltaDeltaH is suggestive of "enthalpic strain" leading to destabilization of antibody-substrate complexes. Together with X-ray structural analyses, the thermodynamic analyses suggest that upon binding the substrate, the antibody alters the conformation of the ester moiety in the substrate from the planar Z form to a thermodynamically unstable twisted conformation, followed by conversion into the transition state. Enthalpic strain also contributes to the transition-state stabilization by destabilizing the ground state, and its degree is much larger for the more efficient catalytic antibody, 6D9.


  • Organizational Affiliation

    Graduate School of Agriculture, Kyoto Prefectural University, 1-5 Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN 6D9A [auth L]219Mus musculusMutation(s): 0 
UniProt
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2NHM3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
IMMUNOGLOBULIN 6D9B [auth H]224Mus musculusMutation(s): 0 
UniProt
Find proteins for P18527 (Mus musculus)
Explore P18527 
Go to UniProtKB:  P18527
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP18527
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CPD
Query on CPD

Download Ideal Coordinates CCD File 
C [auth H][1-(3-DIMETHYLAMINO-PROPYL)-3-ETHYL-UREIDO]-[4-(2,2,2-TRIFLUORO-ACETYLAMINO)-BENZYL]PHOSPHINIC ACID-2-(2,2-DIHYDRO-ACETYLAMINO)-3-HYDROXY-1-(4-NITROPHENYL)-PROPYL ESTER
C28 H36 Cl2 F3 N6 O8 P
SITLNJAUKLVJOA-CTQJRONWSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
CPD Binding MOAD:  2DQT Ki: 50 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.906α = 90
b = 61.662β = 104.68
c = 66.673γ = 90
Software Package:
Software NamePurpose
WEISdata scaling
PROTEINdata reduction
X-PLORmodel building
CNSrefinement
WEISdata reduction
PROTEINdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description