PDBsum entry 3v1d

De novo protein, metal binding protein

PDB id: 3v1d

Contents

Protein chains

(+ 2 more) 48 a.a.

Ligands

1PE ×4

Metals

_CO ×8

Waters ×403

PDB id:

3v1d

Name:

De novo protein, metal binding protein

Title:

Crystal structure of de novo designed mid1-cobalt

Structure:

Computational design, mid1-cobalt. Chain: a, b, c, d, e, f, g, h. Synonym: computational redesign of the biological sequence.. Engineered: yes

Source:

Artificial gene. Organism_taxid: 32630. Expressed in: escherichia coli. Expression_system_taxid: 511693.

Resolution:

1.24Å R-factor: 0.147 R-free: 0.194

Authors:

B.S.Der,M.Machius,M.J.Miley,B.Kuhlman

Key ref:

B.S.Der et al. (2012). Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer. J Am Chem Soc, 134, 375-385. PubMed id: 22092237

Date:

09-Dec-11 Release date: 11-Jan-12

Protein chains

No UniProt id for this chain

Struc: 48 a.a.

J Am Chem Soc 134:375-385 (2012)

PubMed id: 22092237

Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer.

B.S.Der, M.Machius, M.J.Miley, J.L.Mills, T.Szyperski, B.Kuhlman.

ABSTRACT

Computationally designing protein-protein interactions with high affinity and desired orientation is a challenging task. Incorporating metal-binding sites at the target interface may be one approach for increasing affinity and specifying the binding mode, thereby improving robustness of designed interactions for use as tools in basic research as well as in applications from biotechnology to medicine. Here we describe a Rosetta-based approach for the rational design of a protein monomer to form a zinc-mediated, symmetric homodimer. Our metal interface design, named MID1 (NESG target ID OR37), forms a tight dimer in the presence of zinc (MID1-zinc) with a dissociation constant <30 nM. Without zinc the dissociation constant is 4 μM. The crystal structure of MID1-zinc shows good overall agreement with the computational model, but only three out of four designed histidines coordinate zinc. However, a histidine-to-glutamate point mutation resulted in four-coordination of zinc, and the resulting metal binding site and dimer orientation closely matches the computational model (Cα rmsd = 1.4 Å).