4GLV: Obody Am3l09 Bound To Hen Egg-white Lysozyme

The OB-fold is a small, versatile single-domain protein binding module that occurs in all forms of life, where it binds protein, carbohydrate, nucleic acid and small-molecule ligands. We have exploited this natural plasticity to engineer a new class of non-immunoglobulin alternatives to antibodies with unique structural and biophysical characteristics. We present here the engineering of the OB-fold anticodon recognition domain from aspartyl tRNA synthetase taken from the thermophile Pyrobaculum aerophilum. For this single-domain scaffold we have coined the term OBody. Starting from a naive combinatorial library, we engineered an OBody with 3 nM affinity for hen egg-white lysozyme, by optimising the affinity of a naive OBody 11,700-fold over several affinity maturation steps, using phage display. At each maturation step a crystal structure of the engineered OBody in complex with hen egg-white lysozyme was determined, showing binding elements in atomic detail. These structures have given us an unprecedented insight into the directed evolution of affinity for a single antigen on the molecular scale. The engineered OBodies retain the high thermal stability of the parental OB-fold despite mutation of up to 22% of their residues. They can be expressed in soluble form and also purified from bacteria at high yields. They also lack disulfide bonds. These data demonstrate the potential of OBodies as a new scaffold for the engineering of specific binding reagents and provide a platform for further development of future OBody-based applications.
PDB ID: 4GLVDownload
MMDB ID: 112778
PDB Deposition Date: 2012/8/15
Updated in MMDB: 2013/08
Experimental Method:
x-ray diffraction
Resolution: 2.57  Å
Source Organism:
Pyrobaculum aerophilum
Similar Structures:
Biological Unit for 4GLV: dimeric; determined by author
Molecular Components in 4GLV
Label Count Molecule
Proteins (2 molecules)
Lysozyme C(Gene symbol: LYZ)
Molecule annotation
Obody Am3l09
Molecule annotation
Chemicals (6 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB