Solvent water interactions within the active site of the membrane type I matrix metalloproteinase

Matrix metalloproteinases (MMP) are an important family of proteases which catalyze the degradation of extracellular matrix components. While the mechanism of peptide cleavage is well established, the process of enzyme regeneration, which represents the rate limiting step of the catalytic cycle, remains unresolved. This step involves the loss of the newly formed N-terminus (amine) and C-terminus (carboxylate) protein fragments from the site of catalysis coupled with the inclusion of one or more solvent waters. Here we report a novel crystal structure of membrane type I MMP (MT1-MMP or MMP-14), which includes a small peptide bound at the catalytic Zn site via its C-terminus. This structure models the initial product state formed immediately after peptide cleavage but before the final proton transfer to the bound amine; the amine is not present in our system and as such proton transfer cannot occur. Modeling of the protein, including earlier structural data of Bertini and coworkers [I. Bertini, et al., Angew. Chem., Int. Ed., 2006, 45, 7952–7955], suggests that the C-terminus of the peptide is positioned to form an H-bond network to the amine site, which is mediated by a single oxygen of the functionally important Glu240 residue, facilitating efficient proton transfer. Additional quantum chemical calculations complemented with magneto-optical and magnetic resonance spectroscopies clarify the role of two additional, non-catalytic first coordination sphere waters identified in the crystal structure. One of these auxiliary waters acts to stabilize key intermediates of the reaction, while the second is proposed to facilitate C-fragment release, triggered by protonation of the amine. Together these results complete the enzymatic cycle of MMPs and provide new design criteria for inhibitors with improved efficacy.Financial support was provided by the Max Planck Gesellschaft and the Cluster of Excellence RESOLV (EXC 1069) funded by the Deutsche Forschungsgemeinschaft. I. S. is supported by the Binational Science Foundation (BSF) and Israel Science Foundation (ISF). I. S. and M. H. are also supported by the ERC Advanced Grant 695437 THz-Calorimetry. M. G. is an Awardee of the Weizmann Institute of Science National Postdoctoral Award Program for Advancing Women in Science and a recipient of an A. v. Humboldt Fellowship. N. C. acknowledges the support of the Australian Research Council: Future Fellowship (FT140100834). Open Access funding provided by the Max Planck Society

Chemical flexibility of heterobimetallic Mn/Fe cofactors: R2lox and R2c proteins

A heterobimetallic Mn/Fe cofactor is present in the R2 sub-unit of class Ic ribonucleotide reductases (R2c) and in R2-like ligand-binding oxidases (R2lox). Although the protein-derived metal ligands are the same in both groups of proteins, the connectivity of the two metal ions and the chemistry each cofactor performs are different: in R2c, a one-electron oxidant, the Mn/Fe dimer is linked by two oxygen bridges (u-oxo/u-hydroxo), whereas in R2lox, a two-electron oxidant, it is linked by a single oxygen bridge (u-hydroxo) and a fatty acid ligand. Here, we identified a second coordination sphere residue that directs the divergent reactivity of the protein scaffold. We found that the residue that directly precedes the N-terminal carboxylate metal ligand is conserved as a glycine within the R2lox group but not in R2c. Substitution of the glycine with leucine converted the resting-state R2lox cofactor to an R2c-like cofactor, a u-oxo/u-hydroxo–bridged MnIII/FeIII dimer. This species has recently been observed as an intermediate of the oxygen activation reac- tion in WT R2lox, indicating that it is physiologically relevant. Cofactor maturation in R2c and R2lox therefore follows the same pathway, with structural and functional divergence of the two cofactor forms following oxygen activation. We also show that the leucine-substituted variant no longer functions as a two-electron oxidant. Our results reveal that the residue preceding the N-terminal metal ligand directs the cofactor’s reactivity toward one- or two-electron redox chemistry, presumably by setting the protonation state of the bridging oxygens and thereby perturbing the redox potential of the Mn ion.This work was supported by Deutsche Forschungsgemeinschaft Grant Ha3265/6–1 and a Heisenberg Fellowship, German Bundesministerium fu ̈ r Bildung und Forschung Grant 05K14KE1 within the Rontgen-Angstrom Cluster (to M. Haumann), Swedish Research Council Grants 2016-03770 (to J. J. G.) and 2017-04018 (to M. Hogbom), European Research Council Grant HIGH-GEAR 724394, Knut and Alice Wallenberg Foundation Grant 2017.0275, the European Community’s Seventh Framework Programme (FP7/2007–2013) under Grant Agreement 283570 (for BioStruct-X) (to M. Hogbom), and Australian Research Council Future Fellowship FT140100834 (to N. C.)

Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens

Ribonucleotide reductase (RNR) catalyses the only known de novo pathway for the production of all four deoxyribonucleotides that are required for DNA synthesis1,2. It is essential for all organisms that use DNA as their genetic material and is a current drug target3,4. Since the discovery that iron is required for function in the aerobic, class I RNR found in all eukaryotes and many bacteria, a dinuclear metal site has been viewed as necessary to generate and stabilize the catalytic radical that is essential for RNR activity5–7. Here we describe a group of RNR proteins in Mollicutes—including Mycoplasma pathogens—that possess a metal-independent stable radical residing on a modified tyrosyl residue. Structural, biochemical and spectroscopic characterization reveal a stable 3,4-dihydroxyphenylalanine (DOPA) radical species that directly supports ribonucleotide reduction in vitro and in vivo. This observation overturns the presumed requirement for a dinuclear metal site in aerobic ribonucleotide reductase. The metal-independent radical requires new mechanisms for radical generation and stabilization, processes that are targeted by RNR inhibitors. It is possible that this RNR variant provides an advantage under metal starvation induced by the immune system. Organisms that encode this type of RNR—some of which are developing resistance to antibiotics—are involved in diseases of the respiratory, urinary and genital tracts. Further characterization of this RNR family and its mechanism of cofactor generation will provide insight into new enzymatic chemistry and be of value in devising strategies to combat the pathogens that utilize it. We propose that this RNR subclass is denoted class Ie.Financial support to M.H. was provided by the Swedish Research Council (2017-04018), the European Research Council (HIGH-GEAR 724394), and the Knut and Alice Wallenberg Foundation (Wallenberg Academy Fellows (2012.0233 and 2017. 0275)); to B.-M.S. by the Swedish Research Council (2016-01920), the Swedish Cancer Foundation (CAN 2016/670), and the Wenner-Gren Foundations; and to N.C. by the Australian Research Council (FT140100834) and the Max Planck Society. We thank the Diamond Light Source for beamtime (proposals mx11265 and mx15806) and particularly the staff from beamlines I24 and B21