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1. Reaction of O ₂ with a diiron protein generates a mixed-valent Fe ²⁺ /Fe ³⁺ center and peroxide

   https://doi.org/10.1073/pnas.1809913116  

   Bradley, Justin M. ; Svistunenko, Dimitri A. ; Pullin, Jacob ; Hill, Natalie ; Stuart, Rhona K. ; Palenik, Brian ; Wilson, Michael T. ; Hemmings, Andrew M. ; Moore, Geoffrey R. ; Le Brun, Nick E. ( February 2019 , Proceedings of the National Academy of Sciences)

   The gene encoding the cyanobacterial ferritinSynFtn is up-regulated in response to copper stress. Here, we show that, whileSynFtn does not interact directly with copper, it is highly unusual in several ways. First, its catalytic diiron ferroxidase center is unlike those of all other characterized prokaryotic ferritins and instead resembles an animal H-chain ferritin center. Second, as demonstrated by kinetic, spectroscopic, and high-resolution X-ray crystallographic data, reaction of O₂with the di-Fe²⁺center results in a direct, one-electron oxidation to a mixed-valent Fe²⁺/Fe³⁺form. Iron–O₂chemistry of this type is currently unknown among the growing family of proteins that bind a diiron site within a four α-helical bundle in general and ferritins in particular. The mixed-valent form, which slowly oxidized to the more usual di-Fe³⁺form, is an intermediate that is continually generated during mineralization. Peroxide, rather than superoxide, is shown to be the product of O₂reduction, implying that ferroxidase centers function in pairs via long-range electron transfer through the protein resulting in reduction of O₂bound at only one of the centers. We show that electron transfer is mediated by the transient formation of a radical on Tyr40, which lies ∼4 Å from the diiron center. As well as demonstrating an expansion of the iron–O₂chemistry knownmore »to occur in nature, these data are also highly relevant to the question of whether all ferritins mineralize iron via a common mechanism, providing unequivocal proof that they do not.

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2. Evolution of networks of protein domain organization

   https://doi.org/10.1038/s41598-021-90498-8  

   Aziz, M. Fayez ; Caetano-Anollés, Gustavo ( June 2021 , Scientific Reports)

   Domains are the structural, functional and evolutionary units of proteins. They combine to form multidomain proteins. The evolutionary history of this molecular combinatorics has been studied with phylogenomic methods. Here, we construct networks of domain organization and explore their evolution. A time series of networks revealed two ancient waves of structural novelty arising from ancient ‘p-loop’ and ‘winged helix’ domains and a massive ‘big bang’ of domain organization. The evolutionary recruitment of domains was highly modular, hierarchical and ongoing. Domain rearrangements elicited non-random and scale-free network structure. Comparative analyses of preferential attachment, randomness and modularity showed yin-and-yang complementary transition and biphasic patterns along the structural chronology. Remarkably, the evolving networks highlighted a central evolutionary role of cofactor-supporting structures of non-ribosomal peptide synthesis pathways, likely crucial to the early development of the genetic code. Some highly modular domains featured dual response regulation in two-component signal transduction systems with DNA-binding activity linked to transcriptional regulation of responses to environmental change. Interestingly, hub domains across the evolving networks shared the historical role of DNA binding and editing, an ancient protein function in molecular evolution. Our investigation unfolds historical source-sink patterns of evolutionary recruitment that further our understanding of protein architectures and functions.
3. The structure of human CST reveals a decameric assembly bound to telomeric DNA

   https://doi.org/10.1126/science.aaz9649  

   Lim, Ci Ji ; Barbour, Alexandra T. ; Zaug, Arthur J. ; Goodrich, Karen J. ; McKay, Allison E. ; Wuttke, Deborah S. ; Cech, Thomas R. ( June 2020 , Science)

   The CTC1-STN1-TEN1 (CST) complex is essential for telomere maintenance and resolution of stalled replication forks genome-wide. Here, we report the 3.0-angstrom cryo–electron microscopy structure of human CST bound to telomeric single-stranded DNA (ssDNA), which assembles as a decameric supercomplex. The atomic model of the 134-kilodalton CTC1 subunit, built almost entirely de novo, reveals the overall architecture of CST and the DNA-binding anchor site. The carboxyl-terminal domain of STN1 interacts with CTC1 at two separate docking sites, allowing allosteric mediation of CST decamer assembly. Furthermore, ssDNA appears to staple two monomers to nucleate decamer assembly. CTC1 has stronger structural similarity to Replication Protein A than the expected similarity to yeast Cdc13. The decameric structure suggests that CST can organize ssDNA analogously to the nucleosome’s organization of double-stranded DNA.
4. Differential ligand-selective control of opposing enzymatic activities within a bifunctional c-di-GMP enzyme

   https://doi.org/10.1073/pnas.2100657118  

   Patterson, Dayna C. ; Ruiz, Myrrh Perez ; Yoon, Hyerin ; Walker, Johnnie A. ; Armache, Jean-Paul ; Yennawar, Neela H. ; Weinert, Emily E. ( September 2021 , Proceedings of the National Academy of Sciences)

   Cyclic dimeric guanosine monophosphate (c-di-GMP) serves as a second messenger that modulates bacterial cellular processes, including biofilm formation. While proteins containing both c-di-GMP synthesizing (GGDEF) and c-di-GMP hydrolyzing (EAL) domains are widely predicted in bacterial genomes, it is poorly understood how domains with opposing enzymatic activity are regulated within a single polypeptide. Herein, we report the characterization of a globin-coupled sensor protein (GCS) fromPaenibacillus dendritiformis(DcpG) with bifunctional c-di-GMP enzymatic activity. DcpG contains a regulatory sensor globin domain linked to diguanylate cyclase (GGDEF) and phosphodiesterase (EAL) domains that are differentially regulated by gas binding to the heme; GGDEF domain activity is activated by the Fe(II)-NO state of the globin domain, while EAL domain activity is activated by the Fe(II)-O₂state. The in vitro activity of DcpG is mimicked in vivo by the biofilm formation ofP. dendritiformisin response to gaseous environment, with nitric oxide conditions leading to the greatest amount of biofilm formation. The ability of DcpG to differentially control GGDEF and EAL domain activity in response to ligand binding is likely due to the unusual properties of the globin domain, including rapid ligand dissociation rates and high midpoint potentials. Using structural information from small-angle X-ray scattering and negative stain electron microscopy studies,more »we developed a structural model of DcpG, providing information about the regulatory mechanism. These studies provide information about full-length GCS protein architecture and insight into the mechanism by which a single regulatory domain can selectively control output domains with opposing enzymatic activities.

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5. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase

   https://doi.org/10.1038/s41467-022-35021-x  

   King, Edward ; Maxel, Sarah ; Zhang, Yulai ; Kenney, Karissa C. ; Cui, Youtian ; Luu, Emma ; Siegel, Justin B. ; Weiss, Gregory A. ; Luo, Ray ; Li, Han ( November 2022 , Nature Communications)

   Noncanonical cofactor biomimetics (NCBs) such as nicotinamide mononucleotide (NMN⁺) provide enhanced scalability for biomanufacturing. However, engineering enzymes to accept NCBs is difficult. Here, we establish a growth selection platform to evolve enzymes to utilize NMN⁺-based reducing power. This is based on an orthogonal, NMN⁺-dependent glycolytic pathway inEscherichia coliwhich can be coupled to any reciprocal enzyme to recycle the ensuing reduced NMN⁺. With a throughput of >10⁶variants per iteration, the growth selection discovers aLactobacillus pentosusNADH oxidase variant with ~10-fold increase in NMNH catalytic efficiency and enhanced activity for other NCBs. Molecular modeling and experimental validation suggest that instead of directly contacting NCBs, the mutations optimize the enzyme’s global conformational dynamics to resemble the WT with the native cofactor bound. Restoring the enzyme’s access to catalytically competent conformation states via deep navigation of protein sequence space with high-throughput evolution provides a universal route to engineer NCB-dependent enzymes.