1AEF

SPECIFICITY OF LIGAND BINDING TO A BURIED POLAR CAVITY AT THE ACTIVE SITE OF CYTOCHROME C PEROXIDASE (3-AMINOPYRIDINE)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Artificial protein cavities as specific ligand-binding templates: characterization of an engineered heterocyclic cation-binding site that preserves the evolved specificity of the parent protein.

Musah, R.A.Jensen, G.M.Bunte, S.W.Rosenfeld, R.J.Goodin, D.B.

(2002) J Mol Biol 315: 845-857

  • DOI: https://doi.org/10.1006/jmbi.2001.5287
  • Primary Citation of Related Structures:  
    1AEB, 1AED, 1AEE, 1AEF, 1AEG, 1AEH, 1AEJ, 1AEK, 1AEM, 1AEN, 1AEO, 1AEQ

  • PubMed Abstract: 

    Cavity complementation has been observed in many proteins, where an appropriate small molecule binds to a cavity-forming mutant. Here, the binding of compounds to the W191G cavity mutant of cytochrome c peroxidase is characterized by X-ray crystallography and binding thermodynamics. Unlike cavities created by removal of hydrophobic side-chains, the W191G cavity does not bind neutral or hydrophobic compounds, but displays a strong specificity for heterocyclic cations, consistent with the role of the protein to stabilize a tryptophan radical at this site. Ligand dissociation constants for the protonated cationic state ranged from 6 microM for 2-amino-5-methylthiazole to 1 mM for neutral ligands, and binding was associated with a large enthalpy-entropy compensation. X-ray structures show that each of 18 compounds with binding behavior bind specifically within the artificial cavity and not elsewhere in the protein. The compounds make multiple hydrogen bonds to the cavity walls using a subset of the interactions seen between the protein and solvent in the absence of ligand. For all ligands, every atom that is capable of making a hydrogen bond does so with either protein or solvent. The most often seen interaction is to Asp235, and most compounds bind with a specific orientation that is defined by their ability to interact with this residue. Four of the ligands do not have conventional hydrogen bonding atoms, but were nevertheless observed to orient their most polar CH bond towards Asp235. Two of the larger ligands induce disorder in a surface loop between Pro190 and Asn195 that has been identified as a mobile gate to cavity access. Despite the predominance of hydrogen bonding and electrostatic interactions, the small variation in observed binding free energies were not correlated readily with the strength, type or number of hydrogen bonds or with calculated electrostatic energies alone. Thus, as with naturally occurring binding sites, affinities to W191G are likely to be due to a subtle balance of polar, non-polar, and solvation terms. These studies demonstrate how cavity complementation and judicious choice of site can be used to produce a protein template with an unusual ligand-binding specificity.


  • Organizational Affiliation

    Department of Molecular Biology, MB8, 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
MoleculeChains Sequence LengthOrganismDetailsImage
CYTOCHROME C PEROXIDASE294Saccharomyces cerevisiaeMutation(s): 3 
Gene Names: CCP
EC: 1.11.1.5
UniProt
Find proteins for P00431 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P00431 
Go to UniProtKB:  P00431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00431
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
3AP
Query on 3AP

Download Ideal Coordinates CCD File 
C [auth A]3-AMINOPYRIDINE
C5 H7 N2
CUYKNJBYIJFRCU-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108α = 90
b = 77.3β = 90
c = 51.8γ = 90
Software Package:
Software NamePurpose
XTALVIEWrefinement
XENGENdata reduction
XENGENdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-09-04
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-03
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-08-02
    Changes: Refinement description