Skip to main content
U.S. Department of Energy
Office of Scientific and Technical Information

A designed heme-[4Fe-4S] metalloenzyme catalyzes sulfite reduction like the native enzyme

Journal Article · · Science

Multielectron redox reactions often require multicofactor metalloenzymes to facilitate coupled electron and proton movement, but it is challenging to design artificial enzymes to catalyze these important reactions, owing to their structural and functional complexity. We report a designed heteronuclear heme-[4Fe-4S] cofactor in cytochromecperoxidase as a structural and functional model of the enzyme sulfite reductase. The initial model exhibits spectroscopic and ligand-binding properties of the native enzyme, and sulfite reduction activity was improved—through rational tuning of the secondary sphere interactions around the [4Fe-4S] and the substrate-binding sites—to be close to that of the native enzyme. By offering insight into the requirements for a demanding six-electron, seven-proton reaction that has so far eluded synthetic catalysts, this study provides strategies for designing highly functional multicofactor artificial enzymes.

Research Organization:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States)
Sponsoring Organization:
USDOE
DOE Contract Number:
AC05-76RL01830
OSTI ID:
1490222
Report Number(s):
PNNL-SA-138512
Journal Information:
Science, Vol. 361, Issue 6407; ISSN 0036-8075
Publisher:
AAAS
Country of Publication:
United States
Language:
English

References (59)

ATHENA , ARTEMIS , HEPHAESTUS : data analysis for X-ray absorption spectroscopy using IFEFFIT June 2005
Iron-sulfur stoichiometry and structure of iron-sulfur clusters in three-iron proteins: Evidence for [3Fe-4S] clusters January 1983
Structure, Function, and Formation of Biological Iron-Sulfur Clusters June 2005
Unusual Affinity of Cyanide for Ferrous and Ferric Scapharca inaequivalvis Homodimeric Hemoglobin. Equilibria and Kinetics of the Reaction January 1996
Scalable molecular dynamics with NAMD January 2005
Solvent Tuning of Electrochemical Potentials in the Active Sites of HiPIP Versus Ferredoxin November 2007
Iron-Sulfur Clusters: Nature's Modular, Multipurpose Structures August 1997
On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites February 2006
Characterization of the Fundamental Protein Ligand Requirements of [4Fe-4S] 2+/+ Clusters with Sixteen Amino Acid Maquettes October 1998
De novo design of a hyperstable non-natural protein–ligand complex with sub-Å accuracy August 2017
Electron paramagnetic resonance and optical spectroscopic evidence for interaction between siroheme and iron sulfide (Fe4S4) prosthetic groups in Escherichia coli sulfite reductase hemoprotein subunit July 1982
O-S Bond Activation in Structures Isoelectronic with Ferric Peroxide Species Known in O-O-Activating Enzymes: Relevance for Sulfide Activation and Sulfite Reductases: O-S Bond Activation in Ferric-Peroxide-Type Species October 2014
[Fe4S4]- and [Fe3S4]-cluster formation in synthetic peptides November 2011
The Asp-His-iron triad of cytochrome c peroxidase controls the reduction potential electronic structure, and coupling of the tryptophan free radical to the heme April 1993
Synthesis of a [Fe 4 S 4 ]−S−Ferriheme Bridged Assembly Containing an Isobacteriochlorin Component:  A Further Analogue of the Active Site of Sulfite Reductase January 1996
MarkUs: a server to navigate sequence-structure-function space June 2011
Iron-sulfur proteins: spin-coupling model for three-iron clusters. November 1980
Sequence Determination of Reduction Potentials by Cysteinyl Hydrogen Bonds and Peptide Dipoles in [4Fe-4S] Ferredoxins August 2001
Hydrolytic catalysis and structural stabilization in a designed metalloprotein November 2011
Synthesis and Electron Delocalization of [Fe4S4]-S-Fe(III) Bridged Assemblies Related to the Exchange-Coupled Catalytic Site of Sulfite Reductases August 1994
Sulfite Reductase Structure at 1.6  : Evolution and Catalysis for Reduction of Inorganic Anions October 1995
Mutational Analysis of Sulfite Reductase Hemoprotein Reveals the Mechanism for Coordinated Electron and Proton Transfer November 2012
Engineering Cytochrome c Peroxidase into Cytochrome P450:  A Proximal Effect on Heme−Thiolate Ligation August 1999
Density Functional Theory Calculation of Bonding and Charge Parameters for Molecular Dynamics Studies on [FeFe] Hydrogenases March 2009
Bacterial respiration of arsenic and selenium October 1999
Biotinylated Rh(III) Complexes in Engineered Streptavidin for Accelerated Asymmetric C-H Activation October 2012
A Designed Metalloenzyme Achieving the Catalytic Rate of a Native Enzyme September 2015
Enzymic redox chemistry: a proposed reaction pathway for the six-electron reduction of sulfite to sulfide by the assimilatory-type sulfite reductase from Desulfovibrio vulgaris (Hildenborough) September 1991
Crystal structure of catalase HPII from Escherichia coli May 1995
Evidence for siroheme-iron sulfide (Fe4S4) interaction in spinach ferredoxin-sulfite reductase June 1982
Moessbauer study of D. gigas ferredoxin II and spin-coupling model for Fe3S4 cluster with valence delocalization July 1987
Pyridine Hemochromagen Assay for Determining the Concentration of Heme in Purified Protein Solutions January 2015
Crystal Structure of Mycobacterium tuberculosis Catalase-Peroxidase July 2004
Yeast cytochrome c peroxidase. Coordination and spin states of heme prosthetic group. July 1987
Spectroscopic features of cytochrome P450 reaction intermediates March 2011
Spectrophotometric Determination of Hydrogen Sulfide June 1949
Comparison of Cyanide and Carbon Monoxide as Ligands in Iron(II) Porphyrinates June 2009
Siroheme- and [Fe 4 -S 4 ]-dependent NirA from Mycobacterium tuberculosis Is a Sulfite Reductase with a Covalent Cys-Tyr Bond in the Active Site May 2005
Kinetic and crystallographic studies of a redesigned manganese-binding site in cytochrome c peroxidase October 2006
Inhibition of methylene blue formation during determination of the acid-labile sulfide of iron-sulfur protein samples containing dithionite May 1977
Electron paramagnetic resonance and optical evidence for interaction between siroheme and the tetranuclear iron-sulfur center (Fe4S4) prosthetic groups in complexes of Escherichia coli sulfite reductase hemoprotein with added ligands January 1983
Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction July 2010
The relationship between structure and function for the sulfite reductases December 1996
Metalloenzyme design and engineering through strategic modifications of native protein scaffolds April 2014
Probing the Catalytic Mechanism of Sulfite Reductase by X-ray Crystallography:  Structures of the Escherichia coli Hemoprotein in Complex with Substrates, Inhibitors, Intermediates, and Products , October 1997
VASP: A Volumetric Analysis of Surface Properties Yields Insights into Protein-Ligand Binding Specificity August 2010
Infrared Spectroscopy of the Cyanide Complex of Iron(II) Myoglobin and Comparison with Complexes of Microperoxidase and Hemoglobin January 1996
Redox Reactions of the Iron-Sulfur Cluster in a Ribosomal RNA Methyltransferase, RumA: OPTICAL AND EPR STUDIES June 2004
Cyanolysis and spectrophotometric estimation of trithionate in mixture with thiosulfate and tetrathionate June 1969
A bioinspired iron catalyst for nitrate and perchlorate reduction November 2016
Comparison of Cyanide and Carbon Monoxide as Ligands in Iron(II) Porphyrinates June 2009
Crystal structure of yeast cytochrome c peroxidase refined at 1.7-A resolution. November 1984
Artificial Metalloenzymes: Reaction Scope and Optimization Strategies May 2017
Simultaneous Bio-reduction of Nitrate, Perchlorate, Selenate, Chromate, Arsenate, and Dibromochloropropane Using a Hydrogen-based Membrane Biofilm Reactor July 2006
VMD: Visual molecular dynamics February 1996
Characterization of anaerobic sulfite reduction by Salmonella typhimurium and purification of the anaerobically induced sulfite reductase. June 1989
Influence of sulfur oxyanions on reductive dehalogenation activities in Desulfomonile tiedjei. January 1997
Combinedab initio/empirical approach for optimization of Lennard-Jones parameters February 1998
Characterization of a New Type of Dissimilatory Sulfite Reductase Present in Thermodesulfobacterium commune January 1983

Cited By (10)

Unique Tyr-heme double cross-links in F43Y/T67R myoglobin: an artificial enzyme with a peroxidase activity comparable to that of native peroxidases January 2019
Unraveling the enzyme-like activity of heterogeneous single atom catalyst January 2019
Chicken fat for catalysis: a scaffold is as important for molecular complexes for energy transformations as it is for enzymes in catalytic function January 2019
Why does sulfite reductase employ siroheme? January 2019
Rational Design of Artificial Metalloproteins and Metalloenzymes with Metal Clusters July 2019
The importance of catalytic promiscuity for enzyme design and evolution November 2019
Enhancement of protein stability by an additional disulfide bond designed in human neuroglobin January 2019
Artificial Metalloenzymes: Challenges and Opportunities July 2019
Molecular Dynamics Simulation and Kinetic Study of Fluoride Binding to V21C/V66C Myoglobin with a Cytoglobin-like Disulfide Bond April 2020
Reactivity of Small Oxoacids of Sulfur July 2019