Selenium is an essential micronutrient with important functions in human health and relevance to several pathophysiological conditions. The biological effects of selenium are largely mediated by se...

https://www.physiology.org/doi/pdf/10.1152/physrev.00039.2013

Selenoproteins: molecular pathways and physiological roles.

The cellular concentrations of certain metabolites are assiduously monitored to achieve appropriate levels of gene expression. Although proteins have long been known to act as sensors in this capacity, metabolite-binding RNAs, or riboswitches, also play an important role. More than 20 distinct classes of riboswitches have been identified to date, and insights to the molecular recognition strategies of a significant subset of these have been provided by detailed structural studies. This diverse set of metabolite-sensing RNAs is found to exploit a variety of distinct mechanisms to regulate genes that are fundamental to metabolism.

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The structural and functional diversity of metabolite-binding riboswitches.

Mammalian fatty acid synthase is a large multienzyme that catalyzes all steps of fatty acid synthesis. We have determined its crystal structure at 3.2 angstrom resolution covering five catalytic domains, whereas the flexibly tethered terminal acyl carrier protein and thioesterase domains remain unresolved. The structure reveals a complex architecture of alternating linkers and enzymatic domains. Substrate shuttling is facilitated by flexible tethering of the acyl carrier protein domain and by the limited contact between the condensing and modifying portions of the multienzyme, which are mainly connected by linkers rather than direct interaction. The structure identifies two additional nonenzymatic domains: (i) a pseudo-ketoreductase and (ii) a peripheral pseudo-methyltransferase that is probably a remnant of an ancestral methyltransferase domain maintained in some related polyketide synthases. The structural comparison of mammalian fatty acid synthase with modular polyketide synthases shows how their segmental construction allows the variation of domain composition to achieve diverse product synthesis.

The Crystal Structure of a Mammalian Fatty Acid Synthase

GTP-binding (G) proteins constitute a class of P-loop (phosphate-binding loop) proteins that work as molecular switches between the GDP-bound OFF and the GTP-bound ON state. The common principle is the 160–180-residue G domain with an α,β topology that is responsible for nucleotide-dependent conformational changes and drives many biological functions. Although the G domain uses a universally conserved switching mechanism, its structure, function, and GTPase reaction are modified for many different pathways and processes.

Structure-function relationships of the G domain, a canonical switch motif.

Nonribosomal peptide synthetases: structures and dynamics.

We report crystal structures of the 2.6-megadalton α6β6 heterododecameric fatty acid synthase from Thermomyces lanuginosus at 3.1 angstrom resolution. The α and β polypeptide chains form the six catalytic domains required for fatty acid synthesis and numerous expansion segments responsible for extensive intersubunit connections. Detailed views of all active sites provide insights into substrate specificities and catalytic mechanisms and reveal their unique characteristics, which are due to the integration into the multienzyme. The mode of acyl carrier protein attachment in the reaction chamber, together with the spatial distribution of active sites, suggests that iterative substrate shuttling is achieved by a relatively restricted circular motion of the carrier domain in the multifunctional enzyme.

https://science.sciencemag.org/content/sci/316/5822/254.full.pdf

Structure of fungal fatty acid synthase and implications for iterative substrate shuttling.

In the multifunctional fungal fatty acid synthase (FAS), the acyl carrier protein (ACP) domain shuttles reaction intermediates covalently attached to its prosthetic phosphopantetheine group between the different enzymatic centers of the reaction cycle. Here, we report the structure of the Saccharomyces cerevisiae FAS determined at 3.1 angstrom resolution with its ACP stalled at the active site of ketoacyl synthase. The ACP contacts the base of the reaction chamber through conserved, charge-complementary surfaces, which optimally position the ACP toward the catalytic cleft of ketoacyl synthase. The conformation of the prosthetic group suggests a switchblade mechanism for acyl chain delivery to the active site of the enzyme.

https://science.sciencemag.org/content/sci/316/5822/288.full.pdf

Structural Basis for Substrate Delivery by Acyl Carrier Protein in the Yeast Fatty Acid Synthase

In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. Here, we present the X‐ray structures of SelB from the archaeon Methanococcus maripaludis in the apo‐, GDP‐ and GppNHp‐bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl‐binding pocket. All three SelB structures reveal an EF‐Tu:GTP‐like domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational change of the Switch 2 region in the GTPase domain leads to the exposure of SelB residues involved in clamping the 5′ phosphate of the tRNA. A conserved extended loop in domain III of SelB may be responsible for specific interactions with tRNA Sec and act as a ruler for measuring the extra long acceptor arm. Domain IV of SelB adopts a β barrel fold and is flexibly tethered to domain III. The overall domain arrangement of SelB resembles a ‘chalice’ observed so far only for initiation factor IF2/eIF5B. In our model of SelB bound to the ribosome, domain IV points towards the 3′ mRNA entrance cleft ready to interact with the downstream secondary structure element.

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Selenocysteine tRNA-Specific Elongation Factor Selb is a Structural Chimaera of Elongation and Initiation Factors.

The thiamine pyrophosphate (TPP)-sensing riboswitch is the only riboswitch found in eukaryotes In plants, TPP regulates its own production by binding to the 3′ untranslated region of the mRNA encoding ThiC, a critical enzyme in thiamine biosynthesis, which promotes the formation of an unstable splicing variant In order to better understand the molecular basis of TPP-analogue binding to the eukaryotic TPP-responsive riboswitch, we have determined the crystal structures of the Arabidopsis thaliana TPP-riboswitch in complex with oxythiamine pyrophosphate (OTPP) and with the antimicrobial compound pyrithiamine pyrophosphate (PTPP) The OTPP-riboswitch complex reveals that the pyrimidine ring of OTPP is stabilized in its enol form in order to retain key interactions with guanosine 28 of the riboswitch previously observed in the TPP complex The structure of PTPP in complex with the riboswitch shows that the base moiety of guanosine 60 undergoes a conformational change to cradle the pyridine ring of the PTPP

Christian Frick

Papers

Structure of fungal fatty acid synthase and implications for iterative substrate shuttling.

Structural Basis for Substrate Delivery by Acyl Carrier Protein in the Yeast Fatty Acid Synthase

Selenocysteine tRNA-Specific Elongation Factor Selb is a Structural Chimaera of Elongation and Initiation Factors.

Structural basis of thiamine pyrophosphate analogues binding to the eukaryotic riboswitch