1UO3

Structure Based Engineering of Internal Molecular Surfaces Of Four Helix Bundles


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure-Based Engineering of Internal Cavities in Coiled-Coil Peptides

Yadav, M.K.Redman, J.E.Leman, L.J.Alvarez-Gutierrez, J.M.Zhang, Y.Stout, C.D.Ghadiri, M.R.

(2005) Biochemistry 44: 9723

  • DOI: 10.1021/bi050742a
  • Primary Citation of Related Structures:  1UNT, 1UNU, 1UNV, 1UNW, 1UNX, 1UNY, 1UNZ, 1UO0, 1UO1, 1UO2, 1UO4, 1UO5, 1W5G, 1W5I, 2BNI

  • PubMed Abstract: 
  • Cavities and clefts are frequently important sites of interaction between natural enzymes or receptors and their corresponding substrate or ligand molecules and exemplify the types of molecular surfaces that would facilitate engineering of artificial ...

    Cavities and clefts are frequently important sites of interaction between natural enzymes or receptors and their corresponding substrate or ligand molecules and exemplify the types of molecular surfaces that would facilitate engineering of artificial catalysts and receptors. Even so, structural characterizations of designed cavities are rare. To address this issue, we performed a systematic study of the structural effects of single-amino acid substitutions within the hydrophobic cores of tetrameric coiled-coil peptides. Peptides containing single glycine, serine, alanine, or threonine amino acid substitutions at the buried L9, L16, L23, and I26 hydrophobic core positions of a GCN4-based sequence were synthesized and studied by solution-phase and crystallographic techniques. All peptides adopt the expected tetrameric state and contain tunnels or internal cavities ranging in size from 80 to 370 A(3). Two closely related sequences containing an L16G substitution, one of which adopts an antiparallel configuration and one of which adopts a parallel configuration, illustrate that cavities of different volumes and shapes can be engineered from identical core substitutions. Finally, we demonstrate that two of the peptides (L9G and L9A) bind the small molecule iodobenzene when present during crystallization, leaving the general peptide quaternary structure intact but altering the local peptide conformation and certain superhelical parameters. These high-resolution descriptions of varied molecular surfaces within solvent-occluded internal cavities illustrate the breadth of design space available in even closely related peptides and offer valuable models for the engineering of de novo helical proteins.


    Organizational Affiliation

    Department of Chemistry, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GENERAL CONTROL PROTEIN GCN4
A, B
34Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Gene Names: GCN4 (AAS3, ARG9)
Find proteins for P03069 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P03069
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ACE
Query on ACE
A, B
NON-POLYMERC2 H4 O

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.92 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.238 
  • Space Group: P 41 3 2
Unit Cell:
Length (Å)Angle (°)
a = 79.195α = 90.00
b = 79.195β = 90.00
c = 79.195γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
REFMACrefinement
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-10-13
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance