PDBsum entry 1ec5

De novo protein

PDB id: 1ec5

Contents

Protein chains

50 a.a.

Metals

_ZN ×3

Waters ×32

PDB id:

1ec5

Name:

De novo protein

Title:

Crystal structure of four-helix bundle model

Structure:

Protein (four-helix bundle model). Chain: a, b, c. Engineered: yes. Other_details: chemically synthesized

Source:

Synthetic: yes. Other_details: de novo protein design

Biol. unit:

Dimer (from PDB file)

Resolution:

2.50Å R-factor: 0.237 R-free: 0.304

Authors:

S.Geremia

Key ref:

A.Lombardi et al. (2000). Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins. Proc Natl Acad Sci U S A, 97, 6298-6305. PubMed id: 10841536 DOI: 10.1073/pnas.97.12.6298

Date:

25-Jan-00 Release date: 26-Jul-00

Protein chains

No UniProt id for this chain

Struc: 49 a.a.

DOI no: 10.1073/pnas.97.12.6298

Proc Natl Acad Sci U S A 97:6298-6305 (2000)

PubMed id: 10841536

Inaugural article: retrostructural analysis of metalloproteins: application to the design of a minimal model for diiron proteins.

A.Lombardi, C.M.Summa, S.Geremia, L.Randaccio, V.Pavone, W.F.DeGrado.

ABSTRACT

De novo protein design provides an attractive approach for the construction of models to probe the features required for function of complex metalloproteins. The metal-binding sites of many metalloproteins lie between multiple elements of secondary structure, inviting a retrostructural approach to constructing minimal models of their active sites. The backbone geometries comprising the metal-binding sites of zinc fingers, diiron proteins, and rubredoxins may be described to within approximately 1 A rms deviation by using a simple geometric model with only six adjustable parameters. These geometric models provide excellent starting points for the design of metalloproteins, as illustrated in the construction of Due Ferro 1 (DF1), a minimal model for the Glu-Xxx-Xxx-His class of dinuclear metalloproteins. This protein was synthesized and structurally characterized as the di-Zn(II) complex by x-ray crystallography, by using data that extend to 2.5 A. This four-helix bundle protein is comprised of two noncovalently associated helix-loop-helix motifs. The dinuclear center is formed by two bridging Glu and two chelating Glu side chains, as well as two monodentate His ligands. The primary ligands are mostly buried in the protein interior, and their geometries are stabilized by a network of hydrogen bonds to second-shell ligands. In particular, a Tyr residue forms a hydrogen bond to a chelating Glu ligand, similar to a motif found in the diiron-containing R2 subunit of Escherichia coli ribonucleotide reductase and the ferritins. DF1 also binds cobalt and iron ions and should provide an attractive model for a variety of diiron proteins that use oxygen for processes including iron storage, radical formation, and hydrocarbon oxidation.

Selected figure(s)

Figure 2.
Fig. 2. Structure of dimetal ion site in an idealized diiron protein. Two Glu side chains form a bridging interaction between the metal ions, whereas the remaining two carboxylates form a one- or two-coordinate interaction with a single metal ion. Two His side chains are visible behind the ions. Two vacant sites face the viewer and are trans to the His ligands (Right). The figure shows the crystal structure of DF1; carbon atoms are green, nitrogens are blue, oxygens are red, and metal ions are magenta. The backbone trace is shown in purple.

Figure 4.
Fig. 4. Stereo comparison of 2.5 Å di-Zn-DF1 structure with designed model. The superposition of the crystal structure symmetric dimer (green) and the designed model (gray) shows the liganding Glu and His residues. Note that the dimetal-binding site is nearly identical between the model and the crystal structure. However, conformation of the Tyr-2 and Trp-42 side chains in the crystal structure differs markedly from that in the design.

Figures were selected by an automated process.