1M6T

CRYSTAL STRUCTURE OF B562RIL, A REDESIGNED FOUR HELIX BUNDLE

PDB DOI: 10.2210/pdb1M6T/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2002-07-17 Released: 2002-11-06
Deposition Author(s): Chu, R., Takei, J., Knowlton, J.R., Andrykovitch, M., Pei, W., Kajava, A.V., Steinbach, P.J., Ji, X., Bai, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.81 Å
R-Value Free: 0.248
R-Value Work: 0.210

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Redesign of a Four-Helix Bundle Protein by Phage Display Coupled with Proteolysis and Structural Characterization by NMR and X-ray Crystallography

Chu, R., Takei, J., Knowlton, J.R., Andrykovitch, M., Pei, W., Kajava, A.V., Steinbach, P.J., Ji, X., Bai, Y.

(2002) J Mol Biol 323: 253-262

PubMed: 12381319 Search on PubMed
DOI: 10.1016/s0022-2836(02)00884-7
Primary Citation of Related Structures:
1M6T

PubMed Abstract:

To test whether it is practical to use phage display coupled with proteolysis for protein design, we used this approach to convert a partially unfolded four-helix bundle protein, apocytochrome b(562), to a stably folded four-helix bundle protein. Four residues expected to form a hydrophobic core were mutated. One residue was changed to Trp to provide a fluorescence probe for studying the protein's physical properties and to partially fill the void left by the heme. The other three positions were randomly mutated. In addition, another residue in the region to be redesigned was substituted with Arg to provide a specific cutting site for protease Arg-c. This library of mutants was displayed on the surface of phage and challenged with protease Arg-c to select stably folded proteins. The consensus sequence that emerged from the selection included hydrophobic residues at only one of the three positions and non-hydrophobic residues at the other two. Nevertheless, the selected proteins were thermodynamically very stable. The structure of a selected protein was characterized using multi-dimensional NMR. All four helices were formed in the structure. Further, site-directed mutagenesis was used to change one of the two non-hydrophobic residues to a hydrophobic residue, which increased the stability of the protein, indicating that the selection result was not based solely on the protein's global stability and that local structural characteristics may also govern the selection. This conclusion is supported by the crystal structure of another mutant that has two hydrophobic residues substituted for the two non-hydrophobic residues. These results suggest that the hydrophobic interactions in the core are not sufficient to dictate the selection and that the location of the cutting site of the protease also influences the selection of structures.

Organizational Affiliation:

Laboratory of Biochemistry, Building 37, Room 6114E, National Cancer Institute, NIH, Bethesda, MD 20892-4255, USA.

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562	A	106	Escherichia coli	Mutation(s): 3 Gene Names: cytB562, cybC
UniProt
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0ABE7
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction