1A2Y

HEN EGG WHITE LYSOZYME, D18A MUTANT, IN COMPLEX WITH MOUSE MONOCLONAL ANTIBODY D1.3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A mutational analysis of binding interactions in an antigen-antibody protein-protein complex.

Dall'Acqua, W.Goldman, E.R.Lin, W.Teng, C.Tsuchiya, D.Li, H.Ysern, X.Braden, B.C.Li, Y.Smith-Gill, S.J.Mariuzza, R.A.

(1998) Biochemistry 37: 7981-7991

  • DOI: 10.1021/bi980148j

  • PubMed Abstract: 
  • Alanine scanning mutagenesis, double mutant cycles, and X-ray crystallography were used to characterize the interface between the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Twelve out of the 13 nonglycine contact residues on HEL, as det ...

    Alanine scanning mutagenesis, double mutant cycles, and X-ray crystallography were used to characterize the interface between the anti-hen egg white lysozyme (HEL) antibody D1.3 and HEL. Twelve out of the 13 nonglycine contact residues on HEL, as determined by the high-resolution crystal structure of the D1.3-HEL complex, were individually truncated to alanine. Only four positions showed a DeltaDeltaG (DeltaGmutant - DeltaGwild-type) of greater than 1.0 kcal/mol, with HEL residue Gln121 proving the most critical for binding (DeltaDeltaG = 2.9 kcal/mol). These residues form a contiguous patch at the periphery of the epitope recognized by D1.3. To understand how potentially disruptive mutations in the antigen are accommodated in the D1.3-HEL interface, we determined the crystal structure to 1.5 A resolution of the complex between D1.3 and HEL mutant Asp18 --> Ala. This mutation results in a DeltaDeltaG of only 0.3 kcal/mol, despite the loss of a hydrogen bond and seven van der Waals contacts to the Asp18 side chain. The crystal structure reveals that three additional water molecules are stably incorporated in the antigen-antibody interface at the site of the mutation. These waters help fill the cavity created by the mutation and form part of a rearranged solvent network linking the two proteins. To further dissect the energetics of specific interactions in the D1.3-HEL interface, double mutant cycles were carried out to measure the coupling of 14 amino acid pairs, 10 of which are in direct contact in the crystal structure. The highest coupling energies, 2.7 and 2.0 kcal/mol, were measured between HEL residue Gln121 and D1.3 residues VLTrp92 and VLTyr32, respectively. The interaction between Gln121 and VLTrp92 consists of three van der Waals contacts, while the interaction of Gln121 with VLTyr32 is mediated by a hydrogen bond. Surprisingly, however, most cycles between interface residues in direct contact in the crystal structure showed no significant coupling. In particular, a number of hydrogen-bonded residue pairs were found to make no net contribution to complex stabilization. We attribute these results to accessibility of the mutation sites to water, such that the mutated residues exchange their interaction with each other to interact with water. This implies that the strength of the protein-protein hydrogen bonds in these particular cases is comparable to that of the protein-water hydrogen bonds they replace. Thus, the simple fact that two residues are in direct contact in a protein-protein interface cannot be taken as evidence that there necessarily exists a productive interaction between them. Rather, the majority of such contacts may be energetically neutral, as in the D1.3-HEL complex.


    Related Citations: 
    • Hydrogen Bonding and Solvent Structure in an Antigen-Antibody Interface. Crystal Structures and Thermodynamic Characterization of Three Fv Mutants Complexed with Lysozyme
      Fields, B.A.,Goldbaum, F.A.,Dall'Acqua, W.,Malchiodi, E.L.,Cauerhff, A.,Schwarz, F.P.,Ysern, X.,Poljak, R.J.,Mariuzza, R.A.
      (1996) Biochemistry 35: 15494
    • Bound Water Molecules and Conformational Stabilization Help Mediate an Antigen-Antibody Association
      Bhat, T.N.,Bentley, G.A.,Boulot, G.,Greene, M.I.,Tello, D.,Dall'Acqua, W.,Souchon, H.,Schwarz, F.P.,Mariuzza, R.A.,Poljak, R.J.
      (1994) Proc.Natl.Acad.Sci.USA 91: 1089
    • Solvent Rearrangement in an Antigen-Antibody Interface Introduced by Site-Directed Mutagenesis of the Antibody Combining Site
      Ysern, X.,Fields, B.A.,Bhat, T.N.,Goldbaum, F.A.,Dall'Acqua, W.,Schwarz, F.P.,Poljak, R.J.,Mariuzza, R.A.
      (1994) J.Mol.Biol. 238: 496


    Organizational Affiliation

    Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA D1.3 FV (LIGHT CHAIN)
A
107Mus musculusMutation(s): 0 
Find proteins for P01635 (Mus musculus)
Go to UniProtKB:  P01635
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG1-KAPPA D1.3 FV (HEAVY CHAIN)
B
116Mus musculusMutation(s): 0 
Find proteins for P01820 (Mus musculus)
Go to UniProtKB:  P01820
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
C
129Gallus gallusMutation(s): 1 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
C
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.203 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.667α = 90.00
b = 61.212β = 119.14
c = 57.425γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
SCALEPACKdata scaling
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-04-29
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance