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Host protein

6-Phospho-gluconolactonase (6-PGLac) A2A adenosine receptor Adipocyte lipid binding protein (ALBP) Antibody Antibody 03-1 Antibody 12E11G Antibody 13G10 Antibody 13G10 / 14H7 Antibody 14H7 Antibody 1G8 Antibody 28F11 Antibody 38C2 Antibody 3A3 Antibody 7A3 Antibody7G12-A10-G1-A12 Antibody L-chain from Mab13-1 hybridoma cells Antibody SN37.4 Apo-[Fe]-hydrogenase from M. jannaschii Apo-ferritin Apo-HydA1 ([FeFe]-hydrogenase) from C. reinhardtii Apo-HydA enzymes from C. reinhardtii, M. elsdenii, C. pasteurianum Artificial construct Avidin (Av) Azurin Binding domain of Rabenosyn (Rab4) Bovine carbonic anhydrase (CA) Bovine carbonic anhydrase II (CA) Bovine serum albumin (BSA) Bovine β-lactoglobulin (βLG) Bromelain Burkavidin C45 (c-type cytochrome maquette) Carbonic anhydrase (CA) Carboxypeptidase A Catabolite activator protein (CAP) CeuE C-terminal domain of calmodulin Cutinase Cytochrome b562 Cytochrome BM3h Cytochrome c Cytochrome c552 Cytochrome cb562 Cytochrome c peroxidase Cytochrome P450 (CYP119) Domain of Hin recombinase Due Ferro 1 E. coli catabolite gene activator protein (CAP) [FeFe]-hydrogenase from C. pasteurianum (CpI) Ferredoxin (Fd) Ferritin FhuA FhuA ΔCVFtev Flavodoxin (Fld) Glyoxalase II (Human) (gp27-gp5)3 gp45 [(gp5βf)3]2 Heme oxygenase (HO) Hemoglobin Horse heart cytochrome c Horseradish peroxidase (HRP) Human carbonic anhydrase Human carbonic anhydrase II (hCAII) Human retinoid-X-receptor (hRXRa) Human serum albumin (HSA) HydA1 ([FeFe]-hydrogenase) from C. reinhardtii IgG 84A3 Laccase Lipase B from C. antarctica (CALB) Lipase from G. thermocatenulatus (GTL) LmrR Lysozyme Lysozyme (crystal) Mimochrome Fe(III)-S6G(D)-MC6 (De novo designed peptide) Mouse adenosine deaminase Myoglobin (Mb) Neocarzinostatin (variant 3.24) NikA Nitrobindin (Nb) Nitrobindin variant NB4 Nuclease from S. aureus Papain (PAP) Photoactive Yellow Protein (PYP) Photosystem I (PSI) Phytase Prolyl oligopeptidase (POP) Prolyl oligopeptidase (POP) from P. furiosus Rabbit serum albumin (RSA) Ribonuclease S RNase A Rubredoxin (Rd) Silk fibroin fibre Small heat shock protein from M. jannaschii ß-lactoglobulin Staphylococcal nuclease Steroid Carrier Protein 2L (SCP 2L) Sterol Carrier Protein (SCP) Streptavidin (monmeric) Streptavidin (Sav) Thermolysin Thermosome (THS) tHisF TM1459 cupin TRI peptide Trypsin Tryptophan gene repressor (trp) Xylanase A (XynA) Zn8:AB54 Zn8:AB54 (mutant C96T) α3D peptide α-chymotrypsin β-lactamase β-lactoglobulin (βLG)

Corresponding author

Akabori, S. Alberto, R. Albrecht, M. Anderson, J. L. R. Apfel, U.-P. Arnold, F. H. Artero, V. Bäckvall, J. E. Baker, D. Ball, Z. T. Banse, F. Berggren, G. Bian, H.-D. Birnbaum, E. R. Borovik, A. S. Bren, K. L. Bruns, N. Brustad, E. M. Cardona, F. Case, M. A. Cavazza, C. Chan, A. S. C. Coleman, J. E. Craik, C. S. Creus, M. Cuatrecasas, P. Darnall, D. W. DeGrado, W. F. Dervan, P. B. de Vries, J. Diéguez, M. Distefano, M. D. Don Tilley, T. Duhme-Klair, A. K. Ebright, R. H. Emerson, J. P. Eppinger, J. Fasan, R. Filice, M. Fontecave, M. Fontecilla-Camps, J. C. Fruk, L. Fujieda, N. Fussenegger, M. Gademann, K. Gaggero, N. Germanas, J. P. Ghattas, W. Ghirlanda, G. Golinelli-Pimpaneau, B. Goti, A. Gras, E. Gray, H. B. Green, A. P. Gross, Z. Gunasekeram, A. Happe, T. Harada, A. Hartwig, J. F. Hasegawa, J.-Y. Hayashi, T Hemschemeier, A. Herrick, R. S. Hilvert, D. Hirota, S. Huang, F.-P. Hureau, C. Hu, X. Hyster, T. K. Imanaka, T. Imperiali, B. Itoh, S. Janda, K. D. Jarvis, A. G. Jaussi, R. Jeschek, M. Kaiser, E. T. Kamer, P. C. J. Kazlauskas, R. J. Keinan, E. Khare, S. D. Kim, H. S. Kitagawa, S. Klein Gebbink, R. J. M. Kokubo, T. Korendovych, I. V. Kuhlman, B. Kurisu, G. Laan, W. Lee, S.-Y. Lehnert, N. Leow, T. C. Lerner, R. A. Lewis, J. C. Liang, H. Lindblad, P. Lin, Y.-W. Liu, J. Lombardi, A. Lubitz, W. Lu, Y. Maglio, O. Mahy, J.-P. Mangiatordi, G. F. Marchetti, M. Maréchal, J.-D. Marino, T. Marshall, N. M. Matile, S. Matsuo, T. McNaughton, B. R. Ménage, S. Messori, L. Mulfort, K. L. Nastri, F. Nicholas, K. M. Niemeyer, C. M. Nolte, R. J. M. Novič, M. Okamoto, Y. Okano, M. Okuda, J. Onoda, A. Oohora, K. Palomo, J. M. Pàmies, O. Panke, S. Pan, Y. Paradisi, F. Pecoraro, V. L. Pordea, A. Reetz, M. T. Reijerse, E. Renaud, J.-L. Ricoux, R. Rimoldi, I. Roelfes, G. Rovis, T. Sakurai, S. Salmain, M. Sasaki, T. Sauer, D. F. Schultz, P. G. Schwaneberg, U. Seelig, B. Shafaat, H. S. Shahgaldian, P. Sheldon, R. A. Shima, S. Sigman, D. S. Song, W. J. Soumillion, P. Strater, N. Sugiura, Y. Szostak, J. W. Tezcan, F. A. Thorimbert, S. Tiede, D. M. Tiller, J. C. Turner, N. J. Ueno, T. Utschig, L. M. van Koten, G. Wang, J. Ward, T. R. Watanabe, Y. Whitesides, G. M. Wilson, K. S. Woolfson, D. N. Yilmaz, F. Zhang, J.-L.

Journal

3 Biotech Acc. Chem. Res. ACS Catal. ACS Cent. Sci. ACS Sustainable Chem. Eng. Adv. Synth. Catal. Angew. Chem., Int. Ed. Appl. Biochem. Biotechnol. Appl. Organomet. Chem. Artificial Metalloenzymes and MetalloDNAzymes in Catalysis: From Design to Applications Beilstein J. Org. Chem. Biochemistry Biochim. Biophys. Acta, Bioenerg. Biochimie Bioconjug. Chem. Bioorg. Med. Chem. Bioorg. Med. Chem. Lett. Bioorganometallic Chemistry: Applications in Drug Discovery, Biocatalysis, and Imaging Biopolymers Biotechnol. Adv. Biotechnol. Bioeng. Can. J. Chem. Catal. Lett. Catal. Sci. Technol. Cat. Sci. Technol. ChemBioChem ChemCatChem Chem. Commun. Chem. Rev. Chem. Sci. Chem. Soc. Rev. Chem. - Eur. J. Chem. - Asian J. Chem. Lett. ChemistryOpen ChemPlusChem Chimia Commun. Chem. Comprehensive Inorganic Chemistry II Comprehensive Supramolecular Chemistry II C. R. Chim. Coordination Chemistry in Protein Cages: Principles, Design, and Applications Coord. Chem. Rev. Croat. Chem. Acta Curr. Opin. Biotechnol. Curr. Opin. Chem. Biol. Curr. Opin. Struct. Biol. Dalton Trans. Effects of Nanoconfinement on Catalysis Energy Environ. Sci. Eur. J. Biochem. Eur. J. Inorg. Chem. FEBS Lett. Helv. Chim. Acta Inorg. Chim. Acta Inorg. Chem. Int. J. Mol. Sci. Isr. J. Chem. J. Biol. Chem. J. Biol. Inorg. Chem. J. Immunol. Methods J. Inorg. Biochem. J. Mol. Catal. A: Chem. J. Mol. Catal. B: Enzym. J. Organomet. Chem. J. Phys. Chem. Lett. J. Porphyr. Phthalocyanines J. Protein Chem. J. Am. Chem. Soc. J. Chem. Soc. J. Chem. Soc., Chem. Commun. Methods Enzymol. Mol. Divers. Molecular Encapsulation: Organic Reactions in Constrained Systems Nature Nat. Catal. Nat. Chem. Biol. Nat. Chem. Nat. Commun. Nat. Protoc. Nat. Rev. Chem. New J. Chem. Org. Biomol. Chem. Plos ONE Proc. Natl. Acad. Sci. U. S. A. Process Biochem. Prog. Inorg. Chem. Prot. Eng. Protein Engineering Handbook Protein Expression Purif. Pure Appl. Chem. RSC Adv. Science Small Synlett Tetrahedron Tetrahedron: Asymmetry Tetrahedron Lett. Chem. Rec. Top. Catal. Top. Organomet. Chem. Trends Biotechnol.

A De Novo Designed Metalloenzyme for the Hydration of CO2

Protein design will ultimately allow for the creation of artificial enzymes with novel functions and unprecedented stability. To test our current mastery of nature’s approach to catalysis, a ZnII metalloenzyme was prepared using de novo design. α3DH3 folds into a stable single‐stranded three‐helix bundle and binds ZnII with high affinity using His3O coordination. The resulting metalloenzyme catalyzes the hydration of CO2 better than any small molecule model of carbonic anhydrase and with an efficiency within 1400‐fold of the fastest carbonic anhydrase isoform, CAII, and 11‐fold of CAIII.

Metal:

Zn

Ligand type:

Amino acid

Host protein:

α3D peptide

Anchoring strategy:

Dative

Optimization:

Chemical & genetic

Max TON:

---

ee:

---

PDB:

---

Notes:

kcat/KM ≈ 3.8*104 M-1*s-1

A Designed Supramolecular Protein Assembly with In Vivo Enzymatic Activity

The generation of new enzymatic activities has mainly relied on repurposing the interiors of preexisting protein folds because of the challenge in designing functional, three-dimensional protein structures from first principles. Here we report an artificial metallo-β-lactamase, constructed via the self-assembly of a structurally and functionally unrelated, monomeric redox protein into a tetrameric assembly that possesses catalytic zinc sites in its interfaces. The designed metallo-β-lactamase is functional in the Escherichia coli periplasm and enables the bacteria to survive treatment with ampicillin. In vivo screening of libraries has yielded a variant that displays a catalytic proficiency [(kcat/Km)/kuncat] for ampicillin hydrolysis of 2.3 × 106 and features the emergence of a highly mobile loop near the active site, a key component of natural β-lactamases to enable substrate interactions.

Metal:

Zn

Ligand type:

Amino acid

Host protein:

Cytochrome cb562

Anchoring strategy:

Dative

Optimization:

Genetic

Max TON:

---

ee:

---

PDB:

4U9E

Notes:

---

A Highly Specific Metal-Activated Catalytic Antibody

n/a

Metal:

Zn

Ligand type:

Undefined

Host protein:

IgG 84A3

Anchoring strategy:

Undefined

Optimization:

---

Max TON:

---

ee:

---

PDB:

---

Notes:

Substrate specificty

A Metal Ion Regulated Artificial Metalloenzyme

Regulation of enzyme activity is essential in living cells. The rapidly increasing number of designer enzymes with new-to-nature activities makes it necessary to develop novel strategies for controlling their catalytic activity. Here we present the development of a metal ion regulated artificial metalloenzyme created by combining two anchoring strategies, covalent and supramolecular, for introducing a regulatory and a catalytic site, respectively. This artificial metalloenzyme is activated in the presence of Fe2+ ions, but only marginally in the presence of Zn2+.

Metal:

Fe

Ligand type:

Bypyridine

Host protein:

LmrR

Anchoring strategy:

Covalent

Optimization:

Genetic

Max TON:

14

ee:

75

PDB:

---

Notes:

---

Metal:

Zn

Ligand type:

Bypyridine

Host protein:

LmrR

Anchoring strategy:

Covalent

Optimization:

Genetic

Max TON:

6

ee:

80

PDB:

---

Notes:

---

Catalysis by a De Novo Zinc-Mediated Protein Interface: Implications for Natural Enzyme Evolution and Rational Enzyme Engineering

Metal:

Zn

Ligand type:

Amino acid

Anchoring strategy:

Dative

Optimization:

Chemical & genetic

Max TON:

>50

ee:

---

PDB:

3V1C

Notes:

---

Computational Redesign of a Mononuclear Zinc Metalloenzyme for Organophosphate Hydrolysis

Metal:

Zn

Ligand type:

Amino acid

Anchoring strategy:

Dative

Optimization:

Genetic

Max TON:

>140

ee:

---

PDB:

3T1G

Notes:

kcat/KM ≈ 104 M-1*s-1

Design and Evolution of New Catalytic Activity with an Existing Protein Scaffold

Metal:

Zn

Ligand type:

Amino acid

Host protein:

Glyoxalase II (Human)

Anchoring strategy:

Dative

Optimization:

Genetic

Max TON:

---

ee:

---

PDB:

2F50

Notes:

kcat/KM ≈ 184 M-1*s-1

Engineered Metal Regulation of Trypsin Specificity

Metal:

Zn

Ligand type:

Amino acid

Host protein:

Trypsin

Anchoring strategy:

Dative

Optimization:

Genetic

Max TON:

---

ee:

---

PDB:

---

Notes:

Substrate specificty

Metal:

Ni

Ligand type:

Amino acid

Host protein:

Trypsin

Anchoring strategy:

Dative

Optimization:

Genetic

Max TON:

---

ee:

---

PDB:

---

Notes:

Substrate specificty

Hydrolytic Catalysis and Structural Stabilization in a Designed Metalloprotein

Metal:

Hg; Zn

Ligand type:

Amino acid

Host protein:

TRI peptide

Anchoring strategy:

Dative

Optimization:

Chemical & genetic

Max TON:

>10

ee:

---

PDB:

3PBJ

Notes:

Zn ion for catalytic activity, Hg ion for structural stability of the ArM. PDB ID 3PBJ = Structure of an analogue.

Metal:

Hg; Zn

Ligand type:

Amino acid

Host protein:

TRI peptide

Anchoring strategy:

Dative

Optimization:

Chemical & genetic

Max TON:

---

ee:

---

PDB:

3PBJ

Notes:

Zn ion for catalytic activity, Hg ion for structural stability of the ArM, kcat/KM ≈ 1.8*105 M-1*s-1. PDB ID 3PBJ = Structure of an analogue.

Hydrolytic Catalysis and Structural Stabilization in a Designed Metalloprotein

Metal:

Hg; Zn

Ligand type:

Amino acid

Host protein:

TRI peptide

Anchoring strategy:

Dative

Optimization:

Chemical & genetic

Max TON:

>10

ee:

---

PDB:

3PBJ

Notes:

Zn ion for catalytic activity, Hg ion for structural stability of the ArM. PDB ID 3PBJ = Structure of an analogue.

Metal:

Hg; Zn

Ligand type:

Amino acid

Host protein:

TRI peptide

Anchoring strategy:

Dative

Optimization:

Chemical & genetic

Max TON:

---

ee:

---

PDB:

3PBJ

Notes:

Zn ion for catalytic activity, Hg ion for structural stability of the ArM, kcat/KM ≈ 1.8*105 M-1*s-1. PDB ID 3PBJ = Structure of an analogue.

Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-β-Lactamases

Metal:

Zn

Ligand type:

Amino acid

Host protein:

Zn8:AB54

Anchoring strategy:

Dative

Optimization:

Genetic

Reaction:

Hydrolysis

Max TON:

---

ee:

---

PDB:

5XZI

Notes:

Supramolecular protein scaffold constructed from cytochrome cb562 building blocks, Ampicillin hydrolysis: kcat/KM = 130 min-1 * M-1

Metal:

Zn

Ligand type:

Amino acid

Host protein:

Zn8:AB54 (mutant C96T)

Anchoring strategy:

Dative

Optimization:

Genetic

Reaction:

Hydrolysis

Max TON:

---

ee:

---

PDB:

5XZI

Notes:

Supramolecular protein scaffold constructed from cytochrome cb562 building blocks, Ampicillin hydrolysis: kcat/KM = 210 min-1 * M-1

Influence of Active Site Location on Catalytic Activity in De Novo-Designed Zinc Metalloenzymes

Metal:

Hg; Zn

Ligand type:

Amino acid

Host protein:

TRI peptide

Anchoring strategy:

Dative

Optimization:

Chemical & genetic

Max TON:

---

ee:

---

PDB:

3PBJ

Notes:

Influence of position of Zn and Hg ion on catalytic activity of the ArM tested. PDB ID 3PBJ = Structure of an analogue.

Metal Incorporated Horseradish Peroxidase (HRP) Catalyzed Oxidation of Resveratrol: Selective Dimerization or Decomposition

Metal:

Ca; Co; Mn; Ni; Zn

Ligand type:

Undefined

Anchoring strategy:

Undefined

Optimization:

Chemical

Reaction:

Oxidation

Max TON:

---

ee:

---

PDB:

---

Notes:

Oxidation of resveratrol. Dimerisation product obtained.

Multifunctional Nanoenzymes from Carbonic Anhydrase Skeleton

Metal:

Zn

Ligand type:

Amino acid

Host protein:

Carbonic anhydrase (CA)

Anchoring strategy:

Metal substitution

Optimization:

Chemical

Reaction:

Hydrolysis

Max TON:

---

ee:

---

PDB:

---

Notes:

Cross-linked carbonic anhydrase nano-enzyme particles (93 nm in diameter). Hydrolysis of 4-nitrophenyl acetate.

Metal:

Rh

Ligand type:

Amino acid

Host protein:

Carbonic anhydrase (CA)

Anchoring strategy:

Metal substitution

Optimization:

Chemical

Reaction:

Hydration

Max TON:

---

ee:

---

PDB:

---

Notes:

Cross-linked carbonic anhydrase nano-enzyme particles (93 nm in diameter). Hydration of styrene.

Metal:

Mn

Ligand type:

Amino acid

Host protein:

Carbonic anhydrase (CA)

Anchoring strategy:

Metal substitution

Optimization:

Chemical

Reaction:

Oxidation

Max TON:

---

ee:

---

PDB:

---

Notes:

Cross-linked carbonic anhydrase nano-enzyme particles (93 nm in diameter). Oxidation of styrene.

Neocarzinostatin-Based Hybrid Biocatalysts with a RNase like Activity

Metal:

Zn

Ligand type:

Poly-pyridine

Anchoring strategy:

Supramolecular

Optimization:

---

Max TON:

---

ee:

---

PDB:

---

Notes:

kcat/KM = 13.6 M-1 * s-1

Photoinduced Electron Transfer within Supramolecular Hemoprotein Co-Assemblies and Heterodimers Containing Fe and Zn Porphyrins

Metal:

Fe; Zn

Ligand type:

Protoporphyrin IX

Host protein:

Cytochrome b562

Anchoring strategy:

Cystein-maleimide; Supramolecular

Optimization:

Chemical & genetic

Reaction:

Electron transfer

Max TON:

---

ee:

---

PDB:

---

Notes:

---

Selection and Evolution of Enzymes from a Partially Randomized Non-Catalytic Scaffold

Metal:

Zn

Ligand type:

Amino acid

Anchoring strategy:

Dative

Optimization:

Genetic

Reaction:

RNA ligation

Max TON:

>7

ee:

---

PDB:

---

Notes:

---

Sequence-Specific Peptide Cleavage Catalyzed by an Antibody

Metal:

Zn

Ligand type:

Tetramine

Host protein:

Antibody 28F11

Anchoring strategy:

Supramolecular

Optimization:

Chemical

Max TON:

400

ee:

---

PDB:

---

Notes:

---

Structure and Dynamics of a Primordial Catalytic fold Generated by In Vitro Evolution

Metal:

Zn

Ligand type:

Amino acid

Anchoring strategy:

Dative

Optimization:

Genetic

Reaction:

RNA ligation

Max TON:

---

ee:

---

PDB:

2LZE

Notes:

---