2DQU

Crystal form II: 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: 1.70 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1016/j.jmb.2007.03.023
  • Primary Citation of Related Structures:  
    2DQU, 2DQT, 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 antibod ...

    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.


    Related Citations: 
    • Site-directed mutagenesis of active site contact residues in a hydrolytic abzyme: evidence for an essential histidine involved in transition state stabilization
      Miyashita, H., Hara, T., Tanimura, R., Fukuyama, S., Cagnon, C., Kohara, A., Fujii, I.
      (1997) J Mol Biol 267: 1247
    • Correlation between Antigen-Combining-Site Structures and Functions within a Panel of Catalytic Antibodies Generated against a Single Transition State Analog
      Fujii, I., Tanaka, F., Miyashita, H., Tanimura, R., Kinoshita, K.
      (1995) J Am Chem Soc 117: 6199
    • Crystallization and Preliminary X-Ray Analysis: Transition State Complex of a Chloramphenicol Prodrug Activation Specific Catalytic Antibody
      Kristensen, O., Miyashita, H., Vassylyev, D.G., Tanaka, F., Fujii, I., Morikawa, K.
      (1995) Protein Pept Lett 1: 252
    • A common ancestry for multiple catalytic antibodies generated against a single transition-state analog
      Miyashita, H., Hara, T., Tanimura, R., Tanaka, F., Kikuchi, M., Fujii, I.
      (1994) Proc Natl Acad Sci U S A 91: 6045
    • A common ancestry for multiple catalytic antibodies generated against a single transition-state analog
      Miyashita, H., Hara, T., Tamimura, R., Tanaka, F., Kikuchi, M., Fujii, I.
      (1994) Proc Natl Acad Sci U S A 91: 10757
    • Prodrug activation via catalytic antibodies
      Miyashita, H., Karaki, Y., Kikuchi, M., Fujii, I.
      (1993) Proc Natl Acad Sci U S A 90: 5337
    • Thermodynamic and Structural Analyses of Hydrolytic Mechanism by Catalytic Antibodies
      Oda, M., Ito, N., Tsumuraya, T., Suzuki, K., Fujii, I.
      () To be published --: --

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN 6D9L219Mus musculusMutation(s): 0 
Gene Names: IgkcIgk-C
Find proteins for A2NHM3 (Mus musculus)
Explore A2NHM3 
Go to UniProtKB:  A2NHM3
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
IMMUNOGLOBULIN 6D9H224Mus musculusMutation(s): 0 
Find proteins for P18527 (Mus musculus)
Explore P18527 
Go to UniProtKB:  P18527
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CPD
Query on CPD

Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CPDKi:  50   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.7α = 90
b = 63.04β = 98.75
c = 56.56γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • 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