Expression, purification and preliminary crystallographic analysis of bacterial transmembrane protein EfeU for iron import.

The bacterial Efe system functions as an importer of free Fe2+ into cells independently of iron-chelating compounds such as siderophores and consisted of iron-binding protein EfeO, peroxidase EfeB, and transmembrane permease EfeU. While we and other researchers reported crystal structures of EfeO and EfeB, that of EfeU remains undetermined. In this study, we constructed expression system of EfeU derived from Escherichia coli, selected E. coli Rosetta-gami 2 (DE3) as an expression host, and succeeded in purification of the proteins which were indicated to form an oligomer by blue native PAGE. We obtained preliminary data of the X-ray crystallography, suggesting that expression and purification methods we established in this study enable structural analysis of the bacterial Efe system.

Incidence of interstitial lung disease in patients with breast cancer: a nationwide database study in Japan.

Aim: This study estimated the incidence of moderate-to-severe drug-induced interstitial lung disease (ILD) among patients with breast cancer in Japan. Methods: We analyzed a large nationwide database of patients with breast cancer treated with anticancer therapies between 2009 and 2022. ILD was identified using diagnostic codes and treatment records. Results: Of the 81,601 patients, 1042 developed ILD requiring corticosteroids, corresponding to an incidence rate of 1.41 per 100 person-years. The incidence varied across years and treatment regimens. Most ILD incidents occurred within the initial 90-day period post-anticancer therapy initiation. Conclusion: Increase in ILD cases and potential risk variations among treatments underline the importance of continued monitoring, especially during treatment onset, and ILD management in patients with breast cancer undergoing therapy.

This article investigates how often a lung condition known as interstitial lung disease (ILD) occurs in patients treated for breast cancer in Japan. ILD can cause inflammation and damage to the lungs and can be a side effect of some cancer treatments. The study looked at over 81,000 patients with breast cancer from 2009 to 2022. A total of 1042 patients developed ILD that required treatment with steroids to reduce inflammation. This number suggests that ILD occurred in 1.41 out of every 100 patients treated each year. The study noted that the chances of developing ILD varied over the years and depended on the type of cancer treatment. The findings showed that ILD is a risk factor for patients undergoing breast cancer treatment, and the risk can change depending on the treatment they receive. This highlights the importance of doctors keeping a close eye on their patients, especially early in the treatment process, to identify and manage any signs of ILD. Careful monitoring can help improve the health and treatment outcomes of patients with breast cancer. The study also points to the need for more research to understand why ILD occurs and how to prevent or treat it.

A smartphone application for personalized facial aesthetic monitoring.

BACKGROUND: Methods available at home for capturing facial images to track changes in skin quality and evaluate skincare treatments are limited. In this study, we developed a smartphone camera application (app) for personalized facial aesthetic monitoring. MATERIALS AND METHODS: A face alignment indicators (FAIN) system utilizing facial landmark detection, an artificial intelligence technique, to estimate key facial parts, was implemented into the app to maintain a consistent facial appearance during image capture. The FAIN system is composed of a fixed target indicator and an alignment indicator that dynamically changes its shape according to the user's face position, size, and orientation. Users align their faces to match the alignment indicator with the fixed target indicator, and the image is automatically captured when alignment is achieved. RESULTS: We investigated the app's effectiveness in ensuring a consistent facial appearance by analyzing both geometric and colorimetric data. Geometric information from captured faces and colorimetric data from stickers applied to the faces were utilized. The coefficients of variation (CVs) for the L*, a*, and b* values of the stickers were higher compared to those measured by a colorimeter, with CVs of 14.9 times, 8.14 times, and 4.41 times for L*, a*, and b*, respectively. To assess the feasibility of the app for facial aesthetic monitoring, we tracked changes in pseudo-skin color on the cheek of a participant using skin-colored stickers. As a result, we observed the smallest color difference ∆Eab of 1.901, which can be considered as the experimentally validated detection limit using images acquired by the app. CONCLUSION: While the current monitoring method is a relative quantification approach, it contributes to evidence-based evaluations of skincare treatments.

Crystal structures of EfeB and EfeO in a bacterial siderophore-independent iron transport system.

EfeUOB is a siderophore-independent iron uptake mechanism in bacteria. EfeU, EfeO, and EfeB are a permease, an iron-binding or electron-transfer protein, and a peroxidase, respectively. A Gram-negative bacterium, Sphingomonas sp. strain A1, encodes EfeU, EfeO, EfeB together with alginate-binding protein Algp7, a truncated EfeO-like protein (EfeOII), in the genome. The typical EfeO (EfeOI) consists of N-terminal cupredoxin and C-terminal M75 peptidase domains. Here, we detail the structure and function of bacterial EfeB and EfeO. Crystal structures of strain A1 EfeB and Escherichia coli EfeOI were determined at 2.30 Å and 1.85 Å resolutions, respectively. A molecule of heme involved in oxidase activity was bound to the C-terminal Dyp peroxidase domain of EfeB. Two domains of EfeOI were connected by a short loop, and a zinc ion was bound to four residues, Glu156, Glu159, Asp173, and Glu255, in the C-terminal M75 peptidase domain. These residues formed tetrahedron geometry suitable for metal binding and are well conserved among various EfeO proteins including Algp7 (EfeOII), although the metal-binding site (HxxE) is proposed in the C-terminal M75 peptidase domain. This is the first report on structure of a typical EfeO with two domains, postulating a novel metal-binding motif "ExxE-//-D-//-E" in the EfeO C-terminal M75 peptidase domain.

Bacteria with a mouth: Discovery and new insights into cell surface structure and macromolecule transport.

A bacterium with a "mouth"-like pit structure isolated for the first time in the history of microbiology was a Gram-negative rod, containing glycosphingolipids in the cell envelope, and named Sphingomonas sp. strain A1. The pit was dynamic, with repetitive opening and closing during growth on alginate, and directly included alginate concentrated around the pit, particularly by flagellins, an alginate-binding protein localized on the cell surface. Alginate incorporated into the periplasm was subsequently transferred to the cytoplasm by cooperative interactions of periplasmic solute-binding proteins and an ATP-binding cassette transporter in the cytoplasmic membrane. The mechanisms of assembly, functions, and interactions between the above-mentioned molecules were clarified using structural biology. The pit was transplanted into other strains of sphingomonads, and the pitted recombinant cells were effectively applied to the production of bioethanol, bioremediation for dioxin removal, and other tasks. Studies of the function of the pit shed light on the biological significance of cell surface structures and macromolecule transport in bacteria.

4-Deoxy-l-erythro-5-hexoseulose Uronate (DEH) and DEH Reductase: Key Molecule and Enzyme for the Metabolism and Utilization of Alginate.

4-Deoxy-l-erythro-5-hexoseulose uronate (DEH), DEH reductase, and alginate lyase have key roles in the metabolism of alginate, a promising carbon source in brown macroalgae for biorefinery. In contrast to the widely reviewed alginate lyase, DEH and DEH reductase have not been previously reviewed. Here, we summarize the current understanding of DEH and DEH reductase, with emphasis on (i) the non-enzymatic and enzymatic formation and structure of DEH and its reactivity to specific amino groups, (ii) the molecular identification, classification, function, and structure, as well as the structural determinants for coenzyme specificity of DEH reductase, and (iii) the significance of DEH for biorefinery. Improved understanding of this and related fields should lead to the practical utilization of alginate for biorefinery.

The role of calcium binding to the EF-hand-like motif in bacterial solute-binding protein for alginate import.

Gram-negative Sphingomonas sp. A1 incorporates acidic polysaccharide alginate into the cytoplasm via a cell-surface alginate-binding protein (AlgQ2)-dependent ATP-binding cassette transporter (AlgM1M2SS). We investigated the function of calcium bound to the EF-hand-like motif in AlgQ2 by introducing mutations at the calcium-binding site. The X-ray crystallography of the AlgQ2 mutant (D179A/E180A) demonstrated the absence of calcium binding and significant disorder of the EF-hand-like motif. Distinct from the wild-type AlgQ2, the mutant was quite unstable at temperature of strain A1 growth, although unsaturated alginate oligosaccharides stabilized the mutant by formation of substrate/protein complex. In the assay of ATPase and alginate transport by AlgM1M2SS reconstructed in the liposome, the wild-type and mutant AlgQ2 induced AlgM1M2SS ATPase activity in the presence of unsaturated alginate tetrasaccharide. These results indicate that the calcium bound to EF-hand-like motif stabilizes the substrate-unbound AlgQ2 but is not required for the complexation of substrate-bound AlgQ2 and AlgM1M2SS.

Polyunsaturated fatty acids-enriched lipid from reduced sugar alcohol mannitol by marine yeast Rhodosporidiobolus fluvialis Y2.

Brown macroalgae is a promising marine biomass for the production of bioethanol and biodiesel fuels. Here we investigate the biochemical processes used by marine oleaginous yeast for assimilating the major carbohydrate found in brown macroalgae. Briefly, yeast Rhodosporidiobolus fluvialis strain Y2 was isolated from seawater and grown in minimal medium containing reduced sugar alcohol mannitol as the sole carbon source with a salinity comparable to seawater. Conditions limiting nitrogen were used to facilitate lipid synthesis. R. fluvialis Y2 yielded 55.1% (w/w) and 39.1% (w/w) of lipids, per dry cell weight, from mannitol in the absence and presence of salinity, respectively. Furthermore, mannitol, as a sugar source, led to an increase in the composition of polyunsaturated fatty acids, linoleic acid (C18:2) and linolenic acid (C18:3), compared to glucose. This suggests that oxidation of mannitol leads to the activation of NADH-dependent fatty acid desaturases in R. fluvialis Y2. Such fatty acid composition may contribute to the cold-flow properties of biodiesel fuels. Our results identified a salt-tolerant oleaginous yeast species with unique metabolic traits, demonstrating a key role as a decomposer in the global carbon cycle through marine ecosystems. This is the first study on mannitol-induced synthesis of lipids enriched with polyunsaturated fatty acids by marine yeast.

Structural studies on bacterial system used in the recognition and uptake of the macromolecule alginate.

Alginate is an acidic heteropolysaccharide produced by brown seaweed and certain kinds of bacteria. The cells of Sphingomonas sp. strain A1, a gram-negative bacterium, have several alginate-degrading enzymes in their cytoplasm and efficiently utilize this polymer for their growth. Sphingomonas sp. strain A1 cells can directly incorporate alginate into their cytoplasm through a transport system consisting of a "pit" on their cell surface, substrate-binding proteins in their periplasm, and an ATP-binding cassette transporter in their inner membrane. This review deals with the structural and functional aspects of bacterial systems necessary for the recognition and uptake of alginate.

Substrate recognition by bacterial solute-binding protein is responsible for import of extracellular hyaluronan and chondroitin sulfate from the animal host.

Glycosaminoglycans (GAGs) such as hyaluronan and chondroitin in animal extracellular matrices contain disaccharide-repeating units. In a Gram-negative pathogenic Streptobacillus moniliformis, which belongs to Fusobacteria phylum and resides in rodent oral cavities, the solute-binding protein (Smon0123)-dependent ATP-binding cassette transporter imports unsaturated hyaluronan/chondroitin disaccharides into the cytoplasm after GAG lyase-dependent depolymerization. Here we show substrate recognition of unsaturated hyaluronan disaccharide by Smon0123. Moreover, Smon0123 exhibited no affinity for unsaturated chondroitin disaccharides containing three sulfate groups, distinct from non-sulfated, mono-sulfated, and di-sulfated chondroitin disaccharides previously identified as substrates. Crystal structure of Smon0123 with unsaturated hyaluronan disaccharide demonstrates that several residues, including Trp284 and Glu410, are crucial for binding to unsaturated hyaluronan/chondroitin disaccharides, whereas arrangements of water molecules at binding sites are found to be substrate dependent through comparison with substrate-bound structures determined previously. These residues are well conserved in Smon0123-like proteins of fusobacteria, and probably facilitate the fusobacterial residence in hyaluronan-rich oral cavities.

Introduction of integrated dental training jaw models and rubric criteria.

OBJECTIVE: The objective of the present study was to evaluate the effectiveness of introducing integrated jaw models, rubric criteria and homework tasks to a total clinical simulation training course to improve the clinical competence of preclinical dental students. METHODS: A total simulation training course, which involved six clinical dentistry departments, was held for 110 preclinical students in 2014 and 2015. We prepared integrated jaw models having several morbidities along with corresponding medical information and homework tasks. The students formulated diagnoses and devised treatment plans before performing dental treatment on the mannequin under the direction of instructors from the respective clinical departments. Their performance was assessed by both students and instructors using the rubric criteria. RESULTS: Based on quantitative evaluations, the introduction of integrated jaw models appeared to improve the students' ability to formulate diagnoses and devise dental treatment plans and to understand the respective clinical dentistry disciplines. The rubric criteria provided immediate feedback for the students. Based on a comparison of rubric scores, students tended to significantly underestimate their own performance compared with instructors. Moreover, the introduction of homework tasks improved student seriousness. CONCLUSION: Introducing integrated jaw models, rubric criteria and homework tasks to a total simulation training course may be a good approach for improving student performance in terms of dental diagnoses and treatment.

A solute-binding protein in the closed conformation induces ATP hydrolysis in a bacterial ATP-binding cassette transporter involved in the import of alginate.

The Gram-negative bacterium Sphingomonas sp. A1 incorporates alginate into cells via the cell-surface pit without prior depolymerization by extracellular enzymes. Alginate import across cytoplasmic membranes thereby depends on the ATP-binding cassette transporter AlgM1M2SS (a heterotetramer of AlgM1, AlgM2, and AlgS), which cooperates with the periplasmic solute-binding protein AlgQ1 or AlgQ2; however, several details of AlgM1M2SS-mediated alginate import are not well-understood. Herein, we analyzed ATPase and transport activities of AlgM1M2SS after reconstitution into liposomes with AlgQ2 and alginate oligosaccharide substrates having different polymerization degrees (PDs). Longer alginate oligosaccharides (PD ≥ 5) stimulated the ATPase activity of AlgM1M2SS but were inert as substrates of AlgM1M2SS-mediated transport, indicating that AlgM1M2SS-mediated ATP hydrolysis can be stimulated independently of substrate transport. Using X-ray crystallography in the presence of AlgQ2 and long alginate oligosaccharides (PD 6-8) and with the humid air and glue-coating method, we determined the crystal structure of AlgM1M2SS in complex with oligosaccharide-bound AlgQ2 at 3.6 Å resolution. The structure of the ATP-binding cassette transporter in complex with non-transport ligand-bound periplasmic solute-binding protein revealed that AlgM1M2SS and AlgQ2 adopt inward-facing and closed conformations, respectively. These in vitro assays and structural analyses indicated that interactions between AlgM1M2SS in the inward-facing conformation and periplasmic ligand-bound AlgQ2 in the closed conformation induce ATP hydrolysis by the ATP-binding protein AlgS. We conclude that substrate-bound AlgQ2 in the closed conformation initially interacts with AlgM1M2SS, the AlgM1M2SS-AlgQ2 complex then forms, and this formation is followed by ATP hydrolysis.

Sensoring a Generative System to Create User-Controlled Melodies.

The automatic generation of music is an emergent field of research that has attracted the attention of countless researchers. As a result, there is a broad spectrum of state of the art research in this field. Many systems have been designed to facilitate collaboration between humans and machines in the generation of valuable music. This research proposes an intelligent system that generates melodies under the supervision of a user, who guides the process through a mechanical device. The mechanical device is able to capture the movements of the user and translate them into a melody. The system is based on a Case-Based Reasoning (CBR) architecture, enabling it to learn from previous compositions and to improve its performance over time. The user uses a device that allows them to adapt the composition to their preferences by adjusting the pace of a melody to a specific context or generating more serious or acute notes. Additionally, the device can automatically resist some of the user's movements, this way the user learns how they can create a good melody. Several experiments were conducted to analyze the quality of the system and the melodies it generates. According to the users' validation, the proposed system can generate music that follows a concrete style. Most of them also believed that the partial control of the device was essential for the quality of the generated music.

Binding mode of metal ions to the bacterial iron import protein EfeO.

The tripartite EfeUOB system functions as a low pH iron importer in Gram-negative bacteria. In the alginate-assimilating bacterium Sphingomonas sp. strain A1, an additional EfeO-like protein (Algp7) is encoded downstream of the efeUOB operon. Here we show the metal binding mode of Algp7, which carries a M_75 metallopeptidase motif. The Algp7 protein was purified from recombinant E. coli cells and was subsequently characterized using differential scanning fluorimetry, fluorescence spectrometry, atomic absorption spectroscopy, and X-ray crystallography. The fluorescence of a dye, SYPRO Orange, bound to denatured Algp7 in the absence and presence of metal ions was measured during heat treatment. The fluorescence profile of Algp7 in the presence of metals such as ferric, ferrous, and zinc ions, shifted to a higher temperature, suggesting that Algp7 binds these metal ions and that metal ion-bound Algp7 is more thermally stable than the ligand-free form. Algp7 was directly demonstrated to show an ability to bind copper ion by atomic absorption spectroscopy. Crystal structure of metal ion-bound Algp7 revealed that the metal ion is bound to the cleft surrounded by several acidic residues. Four residues, Glu79, Glu82, Asp96, and Glu178, distinct from the M_75 motif (His115xxGlu118), are coordinated to the metal ion. This is the first report to provide structural insights into metal binding by the bacterial EfeO element.

TRAV7-2*02 Expressing CD8⁺ T Cells Are Responsible for Palladium Allergy.

While metallic biomaterials have led to an improvement in the quality of life, metal allergies, especially to palladium (Pd), has caused a recent increase in allergic patients. Metal allergy is known to be a T cell-mediated delayed-type hypersensitivity (DTH); however, the pathogenic T cell subsets and the specific T cell receptor (TCR) have not been identified. Therefore, we attempted to identify the pathogenic T cells responsible for Pd allergy. We found that activating CD8⁺ T cells significantly increased and that the TRAV (TCRα variable) 7-2*02 chain skewed in Pd allergic mice. Furthermore, adoptive transfer experiments revealed that in vitro-cultured Pd-stimulated antigen presenting cells (APCs) function as memory APCs with recipient mice developing Pd allergy and that the frequency of TRAV7-2*02 increases the same as conventional Pd allergic mice. In contrast, neither proliferation of CD8⁺ T cells nor increasing of TRAV7-2*02 was observed in major histocompatibility complex I (MHC I)-deficient Pd-APCs transferred to mice. Taken together, we revealed that TRAV7-2*02-expressing CD8⁺ T cells are the pathogenic T cells for the development of Pd allergy. We also identified the CDR3 consensus motif of pathogenic TCRs as CAAXSGSWQLIF in TRAV7-2*02/TRAJ (TCRα junction)22*01 positive cells. These results suggest that the specific TCRs represent novel targets for the development of diagnostics and treatments for metal allergy.

Metabolic fate of unsaturated glucuronic/iduronic acids from glycosaminoglycans: molecular identification and structure determination of streptococcal isomerase and dehydrogenase.

Glycosaminoglycans in mammalian extracellular matrices are degraded to their constituents, unsaturated uronic (glucuronic/iduronic) acids and amino sugars, through successive reactions of bacterial polysaccharide lyase and unsaturated glucuronyl hydrolase. Genes coding for glycosaminoglycan-acting lyase, unsaturated glucuronyl hydrolase, and the phosphotransferase system are assembled into a cluster in the genome of pathogenic bacteria, such as streptococci and clostridia. Here, we studied the streptococcal metabolic pathway of unsaturated uronic acids and the structure/function relationship of its relevant isomerase and dehydrogenase. Two proteins (gbs1892 and gbs1891) of Streptococcus agalactiae strain NEM316 were overexpressed in Escherichia coli, purified, and characterized. 4-Deoxy-l-threo-5-hexosulose-uronate (Dhu) nonenzymatically generated from unsaturated uronic acids was converted to 2-keto-3-deoxy-d-gluconate via 3-deoxy-d-glycero-2,5-hexodiulosonate through successive reactions of gbs1892 isomerase (DhuI) and gbs1891 NADH-dependent reductase/dehydrogenase (DhuD). DhuI and DhuD enzymatically corresponded to 4-deoxy-l-threo-5-hexosulose-uronate ketol-isomerase (KduI) and 2-keto-3-deoxy-d-gluconate dehydrogenase (KduD), respectively, involved in pectin metabolism, although no or low sequence identity was observed between DhuI and KduI or between DhuD and KduD, respectively. Genes for DhuI and DhuD were found to be included in the streptococcal genetic cluster, whereas KduI and KduD are encoded in clostridia. Tertiary and quaternary structures of DhuI and DhuD were determined by x-ray crystallography. Distinct from KduI ß-barrels, DhuI adopts an α/ß/α-barrel structure as a basic scaffold similar to that of ribose 5-phosphate isomerase. The structure of DhuD is unable to accommodate the substrate/cofactor, suggesting that conformational changes are essential to trigger enzyme catalysis. This is the first report on the bacterial metabolism of glycosaminoglycan-derived unsaturated uronic acids by isomerase and dehydrogenase.

Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity.

Short-chain dehydrogenase/reductase (SDR) is distributed in many organisms, from bacteria to humans, and has significant roles in metabolism of carbohydrates, lipids, amino acids, and other biomolecules. An important intermediate in acidic polysaccharide metabolism is 2-keto-3-deoxy-d-gluconate (KDG). Recently, two short and long loops in Sphingomonas KDG-producing SDR enzymes (NADPH-dependent A1-R and NADH-dependent A1-R') involved in alginate metabolism were shown to be crucial for NADPH or NADH coenzyme specificity. Two SDR family enzymes-KduD from Pectobacterium carotovorum (PcaKduD) and DhuD from Streptococcus pyogenes (SpyDhuD)-prefer NADH as coenzyme, although only PcaKduD can utilize both NADPH and NADH. Both enzymes reduce 2,5-diketo-3-deoxy-d-gluconate to produce KDG. Tertiary and quaternary structures of SpyDhuD and PcaKduD and its complex with NADH were determined at high resolution (approximately 1.6 Å) by X-ray crystallography. Both PcaKduD and SpyDhuD consist of a three-layered structure, α/ß/α, with a coenzyme-binding site in the Rossmann fold; similar to enzymes A1-R and A1-R', both arrange the two short and long loops close to the coenzyme-binding site. The primary structures of the two loops in PcaKduD and SpyDhuD were similar to those in A1-R' but not A1-R. Charge neutrality and moderate space at the binding site of the nucleoside ribose 2' coenzyme region were determined to be structurally crucial for dual-coenzyme specificity in PcaKduD by structural comparison of the NADH- and NADPH-specific SDR enzymes. The corresponding site in SpyDhuD was negatively charged and spatially shallow. This is the first reported study on structural determinants in SDR family KduD related to dual-coenzyme specificity. Proteins 2016; 84:934-947. © 2016 Wiley Periodicals, Inc.

Lateral-typed flagellin responsible for formation of a polar flagellum but not of lateral flagella in Sphingomonas sp. strain A1.

Alginate-assimilating Sphingomonas sp. strain A1 is the Gram-negative bacterium first identified to form a single polar flagellum containing lateral-typed flagellin (p6) in the filament. In addition to the p6 flagellin, two polar-typed flagellins (p5 and p5') are also included in the flagellum. Here we show the significant role of p6 as well as p5/p5' in flagellum formation and cell motility towards alginate. A p6 gene disruptant significantly reduced flagellum formation and it showed no cell motility, whereas each mutant with a disruption in the p5 or p5' gene exhibited cell motility through the formation of a polar flagellum containing p6. The ratio of p6 to p5 decreased in proportion to cell growth, suggesting that strain A1 changes flagellin ratios in the filament depending on the external environment. Each of purified recombinant p5 and p6 proteins formed the filament by in vitro self-assembly and an anti-p5 antibody reacted with the p5 filament but not with the p6 filament. Immunoelectron microscopy using an anti-p5 antibody indicated that strain A1 formed two types of the filament in a single polar flagellum: p6 alone in the entire filament and p5 elongation filament subsequent to the p6 proximal end. Immunoprecipitation with an anti-p5 antibody directly demonstrated that p5 and p6 coexist in a single filament. Strain A1 cells were also found to exhibit a chemotactic motility in response to alginate. This is the first report on function/location of the lateral-typed flagellin in a single polar flagellum and the bacterial chemotaxis towards alginate.

Structure-based conversion of the coenzyme requirement of a short-chain dehydrogenase/reductase involved in bacterial alginate metabolism.

The alginate-assimilating bacterium, Sphingomonas sp. strain A1, degrades the polysaccharides to monosaccharides through four alginate lyase reactions. The resultant monosaccharide, which is nonenzymatically converted to 4-deoxy-L-erythro-5-hexoseulose uronate (DEH), is further metabolized to 2-keto-3-deoxy-D-gluconate by NADPH-dependent reductase A1-R in the short-chain dehydrogenase/reductase (SDR) family. A1-R-deficient cells produced another DEH reductase, designated A1-R', with a preference for NADH. Here, we show the identification of a novel NADH-dependent DEH reductase A1-R' in strain A1, structural determination of A1-R' by x-ray crystallography, and structure-based conversion of a coenzyme requirement in SDR enzymes, A1-R and A1-R'. A1-R' was purified from strain A1 cells and enzymatically characterized. Except for the coenzyme requirement, there was no significant difference in enzyme characteristics between A1-R and A1-R'. Crystal structures of A1-R' and A1-R'·NAD(+) complex were determined at 1.8 and 2.7 Å resolutions, respectively. Because of a 64% sequence identity, overall structures of A1-R' and A1-R were similar, although a difference in the coenzyme-binding site (particularly the nucleoside ribose 2' region) was observed. Distinct from A1-R, A1-R' included a negatively charged, shallower binding site. These differences were caused by amino acid residues on the two loops around the site. The A1-R' mutant with the two A1-R-typed loops maintained potent enzyme activity with specificity for NADPH rather than NADH, demonstrating that the two loops determine the coenzyme requirement, and loop exchange is a promising method for conversion of coenzyme requirement in the SDR family.

Crystal structure of a bacterial unsaturated glucuronyl hydrolase with specificity for heparin.

Extracellular matrix molecules such as glycosaminoglycans (GAGs) are typical targets for some pathogenic bacteria, which allow adherence to host cells. Bacterial polysaccharide lyases depolymerize GAGs in ß-elimination reactions, and the resulting unsaturated disaccharides are subsequently degraded to constituent monosaccharides by unsaturated glucuronyl hydrolases (UGLs). UGL substrates are classified as 1,3- and 1,4-types based on the glycoside bonds. Unsaturated chondroitin and heparin disaccharides are typical members of 1,3- and 1,4-types, respectively. Here we show the reaction modes of bacterial UGLs with unsaturated heparin disaccharides by x-ray crystallography, docking simulation, and site-directed mutagenesis. Although streptococcal and Bacillus UGLs were active on unsaturated heparin disaccharides, those preferred 1,3- rather than 1,4-type substrates. The genome of GAG-degrading Pedobacter heparinus encodes 13 UGLs. Of these, Phep_2830 is known to be specific for unsaturated heparin disaccharides. The crystal structure of Phep_2830 was determined at 1.35-Å resolution. In comparison with structures of streptococcal and Bacillus UGLs, a pocket-like structure and lid loop at subsite +1 are characteristic of Phep_2830. Docking simulations of Phep_2830 with unsaturated heparin disaccharides demonstrated that the direction of substrate pyranose rings differs from that in unsaturated chondroitin disaccharides. Acetyl groups of unsaturated heparin disaccharides are well accommodated in the pocket at subsite +1, and aromatic residues of the lid loop are required for stacking interactions with substrates. Thus, site-directed mutations of the pocket and lid loop led to significantly reduced enzyme activity, suggesting that the pocket-like structure and lid loop are involved in the recognition of 1,4-type substrates by UGLs.