PDBsum entry 1ec5

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protein metals Protein-protein interface(s) links
De novo protein PDB id
Protein chains
50 a.a.
_ZN ×3
Waters ×32
PDB id:
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)
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
25-Jan-00     Release date:   26-Jul-00    
Go to PROCHECK summary

Protein chains
No UniProt id for this chain
Struc: 49 a.a.
Key:    Secondary structure  CATH domain


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.
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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287621 J.E.Donald, D.W.Kulp, and W.F.Degrado (2011).
Salt bridges: Geometrically specific, designable interactions.
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20740227 R.J.Radford, M.Lawrenz, P.C.Nguyen, J.A.McCammon, and F.A.Tezcan (2011).
Porous protein frameworks with unsaturated metal centers in sterically encumbered coordination sites.
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PDB codes: 3nmi 3nmj 3nmk
20017215 J.T.MacDonald, K.Maksimiak, M.I.Sadowski, and W.R.Taylor (2010).
De novo backbone scaffolds for protein design.
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20377257 R.J.Radford, P.C.Nguyen, T.B.Ditri, J.S.Figueroa, and F.A.Tezcan (2010).
Controlled protein dimerization through hybrid coordination motifs.
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PDB code: 3l1m
20225070 R.Torres Martin de Rosales, M.Faiella, E.Farquhar, L.Que, C.Andreozzi, V.Pavone, O.Maglio, F.Nastri, and A.Lombardi (2010).
Spectroscopic and metal-binding properties of DF3: an artificial protein able to accommodate different metal ions.
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19290357 A.F.Peacock, O.Iranzo, and V.L.Pecoraro (2009).
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19637261 A.N.Zaykov, K.R.MacKenzie, and Z.T.Ball (2009).
Controlling peptide structure with coordination chemistry: robust and reversible peptide-dirhodium ligation.
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19090676 C.B.Bell, J.R.Calhoun, E.Bobyr, P.P.Wei, B.Hedman, K.O.Hodgson, W.F.Degrado, and E.I.Solomon (2009).
Spectroscopic definition of the biferrous and biferric sites in de novo designed four-helix bundle DFsc peptides: implications for O2 reactivity of binuclear non-heme iron enzymes.
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18636480 C.Negron, C.Fufezan, and R.L.Koder (2009).
Geometric constraints for porphyrin binding in helical protein binding sites.
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19655393 G.Plascencia-Villa, J.M.Saniger, J.A.Ascencio, L.A.Palomares, and O.T.Ramírez (2009).
Use of recombinant rotavirus VP6 nanotubes as a multifunctional template for the synthesis of nanobiomaterials functionalized with metals.
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19099065 L.Roy, and M.A.Case (2009).
Electrostatic determinants of stability in parallel 3-stranded coiled coils.
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19422060 M.Schneider, X.Fu, and A.E.Keating (2009).
X-ray vs. NMR structures as templates for computational protein design.
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19675646 Y.Lu, N.Yeung, N.Sieracki, and N.M.Marshall (2009).
Design of functional metalloproteins.
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18275812 J.R.Calhoun, W.Liu, K.Spiegel, M.Dal Peraro, M.L.Klein, K.G.Valentine, A.J.Wand, and W.F.DeGrado (2008).
Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.
  Structure, 16, 210-215.
PDB code: 2hz8
18959366 M.Ɓuczkowski, M.Stachura, V.Schirf, B.Demeler, L.Hemmingsen, and V.L.Pecoraro (2008).
Design of thiolate rich metal binding sites within a peptidic framework.
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17609383 D.S.Touw, C.E.Nordman, J.A.Stuckey, and V.L.Pecoraro (2007).
Identifying important structural characteristics of arsenic resistance proteins by using designed three-stranded coiled coils.
  Proc Natl Acad Sci U S A, 104, 11969-11974.
PDB code: 2jgo
17971993 H.E.Huttunen-Hennelly, and J.C.Sherman (2007).
The design, synthesis, and characterization of the first cavitand-based de novo hetero-template-assembled synthetic proteins (Hetero-TASPs).
  Org Biomol Chem, 5, 3637-3650.  
16689627 G.L.Butterfoss, and B.Kuhlman (2006).
Computer-based design of novel protein structures.
  Annu Rev Biophys Biomol Struct, 35, 49-65.  
16819737 H.Wade, S.E.Stayrook, and W.F.Degrado (2006).
The structure of a designed diiron(III) protein: implications for cofactor stabilization and catalysis.
  Angew Chem Int Ed Engl, 45, 4951-4954.  
17140193 J.Hong, O.A.Kharenko, and M.Y.Ogawa (2006).
Incorporating electron-transfer functionality into synthetic metalloproteins from the bottom-up.
  Inorg Chem, 45, 9974-9984.  
17269152 J.Pleiss (2006).
The promise of synthetic biology.
  Appl Microbiol Biotechnol, 73, 735-739.  
16786062 R.L.Koder, and P.L.Dutton (2006).
Intelligent design: the de novo engineering of proteins with specified functions.
  Dalton Trans, (), 3045-3051.  
16478803 Y.Zhang, I.A.Hubner, A.K.Arakaki, E.Shakhnovich, and J.Skolnick (2006).
On the origin and highly likely completeness of single-domain protein structures.
  Proc Natl Acad Sci U S A, 103, 2605-2610.  
15811792 D.Ghosh, and V.L.Pecoraro (2005).
Probing metal-protein interactions using a de novo design approach.
  Curr Opin Chem Biol, 9, 97.  
16156647 D.Noy, B.M.Discher, I.V.Rubtsov, R.M.Hochstrasser, and P.L.Dutton (2005).
Design of amphiphilic protein maquettes: enhancing maquette functionality through binding of extremely hydrophobic cofactors to lipophilic domains.
  Biochemistry, 44, 12344-12354.  
15700297 J.R.Calhoun, F.Nastri, O.Maglio, V.Pavone, A.Lombardi, and W.F.DeGrado (2005).
Artificial diiron proteins: from structure to function.
  Biopolymers, 80, 264-278.  
15698566 M.H.Ali, C.M.Taylor, G.Grigoryan, K.N.Allen, B.Imperiali, and A.E.Keating (2005).
Design of a heterospecific, tetrameric, 21-residue miniprotein with mixed alpha/beta structure.
  Structure, 13, 225-234.
PDB code: 1xof
16091937 O.Maglio, F.Nastri, J.R.Calhoun, S.Lahr, H.Wade, V.Pavone, W.F.DeGrado, and A.Lombardi (2005).
Artificial di-iron proteins: solution characterization of four helix bundles containing two distinct types of inter-helical loops.
  J Biol Inorg Chem, 10, 539-549.  
15763255 P.J.Willcox, C.A.Reinhart-King, S.J.Lahr, W.F.DeGrado, and D.A.Hammer (2005).
Dynamic heterodimer-functionalized surfaces for endothelial cell adhesion.
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15884083 T.Albrecht, W.Li, J.Ulstrup, W.Haehnel, and P.Hildebrandt (2005).
Electrochemical and spectroscopic investigations of immobilized de novo designed heme proteins on metal electrodes.
  Chemphyschem, 6, 961-970.  
15292507 J.Kaplan, and W.F.DeGrado (2004).
De novo design of catalytic proteins.
  Proc Natl Acad Sci U S A, 101, 11566-11570.  
15313244 S.Park, X.Yang, and J.G.Saven (2004).
Advances in computational protein design.
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15056758 S.S.Huang, R.L.Koder, M.Lewis, A.J.Wand, and P.L.Dutton (2004).
The HP-1 maquette: from an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange.
  Proc Natl Acad Sci U S A, 101, 5536-5541.  
12552128 B.T.Farrer, and V.L.Pecoraro (2003).
Hg(II) binding to a weakly associated coiled coil nucleates an encoded metalloprotein fold: a kinetic analysis.
  Proc Natl Acad Sci U S A, 100, 3760-3765.  
12644701 J.T.Welch, W.R.Kearney, and S.J.Franklin (2003).
Lanthanide-binding helix-turn-helix peptides: solution structure of a designed metallonuclease.
  Proc Natl Acad Sci U S A, 100, 3725-3730.  
12876346 L.Di Costanzo, F.Forneris, S.Geremia, and L.Randaccio (2003).
Phasing protein structures using the group-subgroup relation.
  Acta Crystallogr D Biol Crystallogr, 59, 1435-1439.
PDB codes: 1ovu 1ovv
14595023 M.M.Rosenblatt, J.Wang, and K.S.Suslick (2003).
De novo designed cyclic-peptide heme complexes.
  Proc Natl Acad Sci U S A, 100, 13140-13145.
PDB code: 1pbz
12655072 O.Maglio, F.Nastri, V.Pavone, A.Lombardi, and W.F.DeGrado (2003).
Preorganization of molecular binding sites in designed diiron proteins.
  Proc Natl Acad Sci U S A, 100, 3772-3777.
PDB code: 1nvo
12948779 P.D.Barker (2003).
Designing redox metalloproteins from bottom-up and top-down perspectives.
  Curr Opin Struct Biol, 13, 490-499.  
11863465 D.E.Benson, A.E.Haddy, and H.W.Hellinga (2002).
Converting a maltose receptor into a nascent binuclear copper oxygenase by computational design.
  Biochemistry, 41, 3262-3269.  
11959963 E.N.Marsh, and W.F.DeGrado (2002).
Noncovalent self-assembly of a heterotetrameric diiron protein.
  Proc Natl Acad Sci U S A, 99, 5150-5154.  
11316876 A.Pasternak, J.Kaplan, J.D.Lear, and W.F.Degrado (2001).
Proton and metal ion-dependent assembly of a model diiron protein.
  Protein Sci, 10, 958-969.  
11288876 C.Das, S.C.Shankaramma, and P.Balaram (2001).
Molecular carpentry: piecing together helices and hairpins in designed peptides.
  Chemistry, 7, 840-847.  
11282347 G.Xing, and V.J.DeRose (2001).
Designing metal-peptide models for protein structure and function.
  Curr Opin Chem Biol, 5, 196-200.  
11514932 I.L.Karle, D.Ranganathan, and C.Lakshmi (2001).
Demonstration of a cystine unit as a promising turn scaffold for the design of a parallel U-shaped two-helix bundle motif: crystal structure of the homodimer Cys(Aib(n))(2) (n = 3, 4).
  Biopolymers, 59, 301-304.  
11500872 M.Merkx, D.A.Kopp, M.H.Sazinsky, J.L.Blazyk, J.Müller, and S.J.Lippard (2001).
Dioxygen Activation and Methane Hydroxylation by Soluble Methane Monooxygenase: A Tale of Two Irons and Three Proteins A list of abbreviations can be found in Section 7.
  Angew Chem Int Ed Engl, 40, 2782-2807.  
11050226 A.Lombardi, D.Marasco, O.Maglio, L.Di Costanzo, F.Nastri, and V.Pavone (2000).
Miniaturized metalloproteins: application to iron-sulfur proteins.
  Proc Natl Acad Sci U S A, 97, 11922-11927.  
11304672 J.Fernandez-Carneado, D.Grell, P.Durieux, J.Hauert, T.Kovacsovics, and G.Tuchscherer (2000).
Surface grafting onto template-assembled synthetic protein scaffolds in molecular recognition.
  Biopolymers, 55, 451-458.  
  11206050 P.Burkhard, M.Meier, and A.Lustig (2000).
Design of a minimal protein oligomerization domain by a structural approach.
  Protein Sci, 9, 2294-2301.
PDB code: 1hqj
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.