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1. Structure of the E. coli agmatinase, SPEB

   https://doi.org/10.1371/journal.pone.0248991  

   Chitrakar, Iva ; Ahmed, Syed Fardin ; Torelli, Andrew T. ; French, Jarrod B. ( April 2021 , PLOS ONE)

   Permyakov, Eugene A. (Ed.)

   Agmatine amidinohydrolase, or agmatinase, catalyzes the conversion of agmatine to putrescine and urea. This enzyme is found broadly across kingdoms of life and plays a critical role in polyamine biosynthesis and the regulation of agmatine concentrations. Here we describe the high-resolution X-ray crystal structure of the E . coli agmatinase, SPEB. The data showed a relatively high degree of pseudomerohedral twinning, was ultimately indexed in the P 3 1 space group and led to a final model with eighteen chains, corresponding to three full hexamers in the asymmetric unit. There was a solvent content of 38.5% and refined R/R free values of 0.166/0.216. The protein has the conserved fold characteristic of the agmatine ureohydrolase family and displayed a high degree of structural similarity among individual protomers. Two distinct peaks of electron density were observed in the active site of most of the eighteen chains of SPEB. As the activity of this protein is known to be dependent upon manganese and the fold is similar to other dinuclear metallohydrolases, these peaks were modeled as manganese ions. The orientation of the conserved active site residues, in particular those amino acids that participate in binding the metal ions and a pair of acidicmore »residues (D153 and E274 in SPEB) that play a role in catalysis, are similar to other agmatinase and arginase enzymes and is consistent with a hydrolytic mechanism that proceeds via a metal-activated hydroxide ion.« less
2. Tuning of p K_a values activates substrates in flavin-dependent aromatic hydroxylases

   https://doi.org/10.1074/jbc.RA119.011884  

   Pitsawong, Warintra ; Chenprakhon, Pirom ; Dhammaraj, Taweesak ; Medhanavyn, Dheeradhach ; Sucharitakul, Jeerus ; Tongsook, Chanakan ; van Berkel, Willem J. ; Chaiyen, Pimchai ; Miller, Anne-Frances ( March 2020 , Journal of Biological Chemistry)

   Hydroxylation of substituted phenols by flavin-dependent monooxygenases is the first step of their biotransformation in various microorganisms. The reaction is thought to proceed via electrophilic aromatic substitution, catalyzed by enzymatic deprotonation of substrate, in single-component hydroxylases that use flavin as a cofactor (group A). However, two-component hydroxylases (group D), which use reduced flavin as a co-substrate, are less amenable to spectroscopic investigation. Herein, we employed 19 F NMR in conjunction with fluorinated substrate analogs to directly measure p K a values and to monitor protein events in hydroxylase active sites. We found that the single-component monooxygenase 3-hydroxybenzoate 6-hydroxylase (3HB6H) depresses the p K a of the bound substrate analog 4-fluoro-3-hydroxybenzoate (4F3HB) by 1.6 pH units, consistent with previously proposed mechanisms. 19 F NMR was applied anaerobically to the two-component monooxygenase 4-hydroxyphenylacetate 3-hydroxylase (HPAH), revealing depression of the p K a of 3-fluoro-4-hydroxyphenylacetate by 2.5 pH units upon binding to the C 2 component of HPAH. 19 F NMR also revealed a p K a of 8.7 ± 0.05 that we attributed to an active-site residue involved in deprotonating bound substrate, and assigned to His-120 based on studies of protein variants. Thus, in both types of hydroxylases, we confirmed that bindingmore »favors the phenolate form of substrate. The 9 and 14 kJ/mol magnitudes of the effects for 3HB6H and HPAH-C 2 , respectively, are consistent with p K a tuning by one or more H-bonding interactions. Our implementation of 19 F NMR in anaerobic samples is applicable to other two-component flavin-dependent hydroxylases and promises to expand our understanding of their catalytic mechanisms.« less
3. Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires

   https://doi.org/10.3390/nano10112143  

   Marzolf, Daniel R. ; McKenzie, Aidan M. ; O’Malley, Matthew C. ; Ponomarenko, Nina S. ; Swaim, Coleman M. ; Brittain, Tyler J. ; Simmons, Natalie L. ; Pokkuluri, Phani Raj ; Mulfort, Karen L. ; Tiede, David M. ; et al ( November 2020 , Nanomaterials)

   Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4–8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small,more »experimentally versatile photosynthetic biohybrid assemblies.« less
4. Melamine-based functionalized graphene oxide and zirconium phosphate for high performance removal of mercury and lead ions from water

   https://doi.org/10.1039/d0ra07546a  

   Bakry, Ayyob M. ; Awad, Fathi S. ; Bobb, Julian A. ; Ibrahim, Amr A. ; El-Shall, M. Samy ( October 2020 , RSC Advances)

   Heavy metal ions are highly toxic and widely spread as environmental pollutants. This work reports the development of two novel chelating adsorbents, based on the chemical modifications of graphene oxide and zirconium phosphate by functionalization with melamine-based chelating ligands for the effective and selective extraction of Hg( ii ) and Pb( ii ) from contaminated water sources. The first adsorbent melamine, thiourea-partially reduced graphene oxide (MT-PRGO) combines the heavier donor atom sulfur with the amine and triazine nitrogen's functional groups attached to the partially reduced GO nanosheets to effectively capture Hg( ii ) ions from water. The MT-PRGO adsorbent shows high efficiency for the extraction of Hg( ii ) with a capacity of 651 mg g −1 and very fast kinetics resulting in a 100% removal of Hg( ii ) from 500 ppb and 50 ppm concentrations in 15 second and 30 min, respectively. The second adsorbent, melamine zirconium phosphate (M-ZrP), is designed to combine the amine and triazine nitrogen's functional groups of melamine with the hydroxyl active sites of zirconium phosphate to effectively capture Pb( ii ) ions from water. The M-ZrP adsorbent shows exceptionally high adsorption affinity for Pb( ii ) with a capacity of 681 mg gmore »−1 and 1000 mg g −1 using an adsorbent dose of 1 g L −1 and 2 g L −1 , respectively. The high adsorption capacity is also coupled with fast kinetics where the equilibrium time required for the 100% removal of Pb( ii ) from 1 ppm, 100 ppm and 1000 ppm concentrations is 40 seconds, 5 min and 30 min, respectively using an adsorbent dose of 1 g L −1 . In a mixture of six heavy metal ions at a concentration of 10 ppm, the removal efficiency is 100% for Pb( ii ), 99% for Hg( ii ), Cd( ii ) and Zn( ii ), 94% for Cu( ii ), and 90% for Ni( ii ) while at a higher concentration of 250 ppm the removal efficiency for Pb( ii ) is 95% compared to 23% for Hg( ii ) and less than 10% for the other ions. Because of the fast adsorption kinetics, high removal capacity, excellent regeneration, stability and reusability, the MT-PRGO and M-ZrP are proposed as top performing remediation adsorbents for the solid phase extraction of Hg( ii ) and Pb( ii ), respectively from contaminated water.« less
5. Structural basis for an unprecedented enzymatic alkylation in cylindrocyclophane biosynthesis

   https://doi.org/10.7554/eLife.75761  

   Braffman, Nathaniel R ; Ruskoski, Terry B ; Davis, Katherine M ; Glasser, Nathaniel R ; Johnson, Cassidy ; Okafor, C Denise ; Boal, Amie K ; Balskus, Emily P ( February 2022 , eLife)

   The cyanobacterial enzyme CylK assembles the cylindrocyclophane natural products by performing two unusual alkylation reactions, forming new carbon–carbon bonds between aromatic rings and secondary alkyl halide substrates. This transformation is unprecedented in biology, and the structure and mechanism of CylK are unknown. Here, we report X-ray crystal structures of CylK, revealing a distinctive fusion of a Ca 2+ -binding domain and a β-propeller fold. We use a mutagenic screening approach to locate CylK’s active site at its domain interface, identifying two residues, Arg105 and Tyr473, that are required for catalysis. Anomalous diffraction datasets collected with bound bromide ions, a product analog, suggest that these residues interact with the alkyl halide electrophile. Additional mutagenesis and molecular dynamics simulations implicate Asp440 in activating the nucleophilic aromatic ring. Bioinformatic analysis of CylK homologs from other cyanobacteria establishes that they conserve these key catalytic amino acids, but they are likely associated with divergent reactivity and altered secondary metabolism. By gaining a molecular understanding of this unusual biosynthetic transformation, this work fills a gap in our understanding of how alkyl halides are activated and used by enzymes as biosynthetic intermediates, informing enzyme engineering, catalyst design, and natural product discovery.