Structural, kinetic, and evolutionary peculiarities of HISN3, a plant 5'-ProFAR isomerase.

Histidine biosynthesis is essential for the growth and development of plants, where it occurs within chloroplasts. The eleven reactions are catalyzed by eight enzymes, known as HISN1-8, each acting sequentially. Here, we present the crystal structures of a 5'-ProFAR isomerase (HISN3) from the model legume Medicago truncatula bound to its enzymatically synthesized substrate (ProFAR) and product (PrFAR).

Legume-type glutamate dehydrogenase: Structure, activity, and inhibition studies.

Glutamate dehydrogenases (GDHs) are key enzymes at the crossroads of N and C metabolism in plants. Legumes, whose N metabolism is particularly intricate, possess a unique type of GDH. This study presents an analysis of a legume-type GDH (isoform 2) from Medicago truncatula (MtGDH2).

[Advancements in Structural Biology – How to See Molecules of Life?].

Structural biology is focused on understanding the architecture of biomolecules, such as proteins and nucleic acids. Deciphering the structure helps to understand their function in the cell at a very precise – molecular level. This makes it possible to not only determine the basis of diseases but also to propose therapeutic strategies and tools.

Targeting imidazole-glycerol phosphate dehydratase in plants: novel approach for structural and functional studies, and inhibitor blueprinting.

The histidine biosynthetic pathway (HBP) is targeted for herbicide design with preliminary success only regarding imidazole-glycerol phosphate dehydratase (IGPD, EC 4.2.1.

Structural and functional studies of Arabidopsis thaliana glutamate dehydrogenase isoform 2 demonstrate enzyme dynamics and identify its calcium binding site.

Glutamate dehydrogenase (GDH) is an enzyme at the crossroad of plant nitrogen and carbon metabolism. GDH catalyzes the conversion of 2-oxoglutarate into glutamate (2OG → Glu), utilizing ammonia as cosubstrate and NADH as coenzyme. The GDH reaction is reversible, meaning that the NAD-dependent reaction (Glu → 2OG) releases ammonia.

Impaired interactions of ataxin-3 with protein complexes reveals their specific structure and functions in SCA3 Ki150 model.

Spinocerebellar ataxia type 3 (SCA3/MJD) is a neurodegenerative disease caused by CAG expansion in mutant gene. The resulting PolyQ tract in mutant ataxin-3 protein is toxic to neurons and currently no effective treatment exists. Function of both normal and mutant ataxin-3 is pleiotropic by their interactions and the influence on protein level.

Insights into the substrate specificity, structure, and dynamics of plant histidinol-phosphate aminotransferase (HISN6).

Histidinol-phosphate aminotransferase is the sixth protein (hence HISN6) in the histidine biosynthetic pathway in plants. HISN6 is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of imidazole acetol phosphate into L-histidinol phosphate (HOLP). Here, we show that plant HISN6 enzymes are closely related to the orthologs from Chloroflexota.

Functional Characterization of P5C Reductase, the Enzyme at the Converging Point of Proline and Arginine Metabolism.

The enzyme that, in catalyzes the last step in both proline synthesis and arginine catabolism, δ-pyrroline-5-carboxylate (P5C) reductase, was purified to near homogeneity and characterized thoroughly. Retention patterns upon gel permeation chromatography were consistent with a homodecameric composition of the holomer. High lability of the purified preparations and stabilization by reducing compounds suggested susceptibility to reactive-oxygen-species-mediated damage.

Arabidopsis thaliana serine hydroxymethyltransferases: functions, structures, and perspectives.

Serine hydroxymethyltransferase (SHM) is one of the hallmarks of one-carbon metabolism. In plants, isoforms of SHM participate in photorespiration and/or transfer the one-carbon unit from L-serine to tetrahydrofolate (THF), hence producing 5,10-CH-THF that is needed, e.g.

New aspects of DNA recognition by group II WRKY transcription factor revealed by structural and functional study of AtWRKY18 DNA binding domain.

WRKY transcription factors (TFs) constitute one of the largest families of plant TFs. Based on the organization of domains and motifs, WRKY TFs are divided into three Groups (I-III). The WRKY subgroup IIa includes three representatives in A.

Deciphering the structure of 5--pyruvyl-shikimate-3-phosphate synthase: An essential step toward the discovery of novel inhibitors to supersede glyphosate.

Glyphosate interferes with plant aromatic metabolism through the inhibition of 5--pyruvyl-shikimate-3-phosphate (EPSP) synthase [EPSPS, EC 2.5.1.

Cryo-EM reconstructions of BMV-derived virus-like particles reveal assembly defects in the icosahedral lattice structure.

The increasing interest in virus-like particles (VLPs) has been reflected by the growing number of studies on their assembly and application. However, the formation of complete VLPs is a complex phenomenon, making it difficult to rationally design VLPs with desired features . In this paper, we describe VLPs assembled from the recombinant capsid protein of brome mosaic virus (BMV).

Structural Insights Into the 5'UG/3'GU Wobble Tandem in Complex With Ba Cation.

G•U wobble base pair frequently occurs in RNA structures. The unique chemical, thermodynamic, and structural properties of the G•U pair are widely exploited in RNA biology. In several RNA molecules, the G•U pair plays key roles in folding, ribozyme catalysis, and interactions with proteins.

3D Domain Swapping Dimerization of the Receiver Domain of Cytokinin Receptor CRE1 From and .

Cytokinins are phytohormones regulating many biological processes that are vital to plants. CYTOKININ RESPONSE1 (CRE1), the main cytokinin receptor, has a modular architecture composed of a cytokinin-binding CHASE (Cyclases/Histidine kinases Associated Sensory Extracellular) domain, followed by a transmembrane fragment, an intracellular histidine kinase (HK) domain, and a receiver domain (REC). Perception of cytokinin signaling involves (i) a hormone molecule binding to the CHASE domain, (ii) CRE1 autophosphorylation at a conserved His residue in the HK domain, followed by a phosphorelay to (iii) a conserved Asp residue in the REC domain, (iv) a histidine-containing phosphotransfer protein (HPt), and (v) a response regulator (RR).

Structural and biochemical insights into CRISPR RNA processing by the Cas5c ribonuclease SMU1763 from Streptococcus mutans.

The cariogenic pathogen Streptococcus mutans contains two CRISPR systems (type I-C and type II-A) with the Cas5c protein (SmuCas5c) involved in processing of long CRISPR RNA transcripts (pre-crRNA) containing repeats and spacers to mature crRNA guides. In this study, we determined the crystal structure of SmuCas5c at a resolution of 1.72 Å, which revealed the presence of an N-terminal modified RNA recognition motif and a C-terminal twisted β-sheet domain with four bound sulphate molecules.

Peculiar substrate specificity of δ-pyrroline-5-carboxylate reductase in the obligately fermentative bacterium Zymomonas mobilis.

Background: The enzyme that catalyzes the last step in proline synthesis, δ-pyrroline-5-carboxylate reductase, showed in most cases a distinct preference in vitro for NADPH as the electron donor.

Methods And Results: A Zymomonas mobilis gene coding for a δ-pyrroline-5-carboxylate reductase was cloned and heterologously expressed, and the recombinant protein was purified and characterized. The enzyme showed higher affinity to, and higher catalytic rate with NADH, with a specific activity of about 600 nkat (mg protein).

Structural and mechanistic insights into the bifunctional HISN2 enzyme catalyzing the second and third steps of histidine biosynthesis in plants.

The second and third steps of the histidine biosynthetic pathway (HBP) in plants are catalyzed by a bifunctional enzyme-HISN2. The enzyme consists of two distinct domains, active respectively as a phosphoribosyl-AMP cyclohydrolase (PRA-CH) and phosphoribosyl-ATP pyrophosphatase (PRA-PH). The domains are analogous to single-domain enzymes encoded by bacterial hisI and hisE genes, respectively.

Serendipitous crystallization of E. coli HPII catalase, a sequel to "the tale usually not told".

Protein crystallographers are well aware of the trap of crystallizing E. coli proteins instead of the macromolecule of interest if heterologous recombinant protein expression in E. coli was part of the experimental pipeline.

Base pairing, structural and functional insights into N4-methylcytidine (m4C) and N4,N4-dimethylcytidine (m42C) modified RNA.

The N4-methylation of cytidine (m4C and m42C) in RNA plays important roles in both bacterial and eukaryotic cells. In this work, we synthesized a series of m4C and m42C modified RNA oligonucleotides, conducted their base pairing and bioactivity studies, and solved three new crystal structures of the RNA duplexes containing these two modifications. Our thermostability and X-ray crystallography studies, together with the molecular dynamic simulation studies, demonstrated that m4C retains a regular C:G base pairing pattern in RNA duplex and has a relatively small effect on its base pairing stability and specificity.

Structural Studies of Glutamate Dehydrogenase (Isoform 1) From , an Important Enzyme at the Branch-Point Between Carbon and Nitrogen Metabolism.

Glutamate dehydrogenase (GDH) releases ammonia in a reversible NAD(P)-dependent oxidative deamination of glutamate that yields 2-oxoglutarate (2OG). In current perception, GDH contributes to Glu homeostasis and plays a significant role at the junction of carbon and nitrogen assimilation pathways. GDHs are members of a superfamily of ELFV (Glu/Leu/Phe/Val) amino acid dehydrogenases and are subdivided into three subclasses, based on coenzyme specificity: NAD-specific, NAD/NADP dual-specific, and NADP-specific.

Structural and kinetic properties of serine hydroxymethyltransferase from the halophytic cyanobacterium Aphanothece halophytica provide a rationale for salt tolerance.

Serine hydroxymethyltransferase (SHMT) is a pyridoxal 5'-phosphate-dependent enzyme that plays a pivotal role in cellular one‑carbon metabolism. In plants and cyanobacteria, this enzyme is also involved in photorespiration and confers salt tolerance, as in the case of SHMT from the halophilic cyanobacterium Aphanothece halophytica (AhSHMT). We have characterized the catalytic properties of AhSHMT in different salt and pH conditions.

S-adenosylmethionine synthases in plants: Structural characterization of type I and II isoenzymes from Arabidopsis thaliana and Medicago truncatula.

S-adenosylmethionine synthases (MATs) are responsible for production of S-adenosylmethionine, the cofactor essential for various methylation reactions, production of polyamines and phytohormone ethylene, etc. Plants have two distinct MAT types (I and II). This work presents the structural analysis of MATs from Arabidopsis thaliana (AtMAT1 and AtMAT2, both type I) and Medicago truncatula (MtMAT3a, type II), which, unlike most MATs from other domains of life, are dimers where three-domain subunits are sandwiched flat with one another.