scholarly journals Structure based engineering for substrate specificity of pinoresinol-lariciresinol reductases

2020 ◽  
Author(s):  
Ying Xiao ◽  
Kai Shao ◽  
Jingwen Zhou ◽  
Lian Wang ◽  
Di Wu ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Molecular Mechanism ◽  
Large Scale ◽  
Structural Diversity ◽  
Commercial Production ◽  
Structural Elements ◽  
Substrate Specificities ◽  
Lignan Biosynthesis ◽  
Binding Forms ◽  
Insight Into

Abstract Pinoresinol–lariciresinol reductases (PLR) are enzymes involved in the lignan biosynthesis after the initial dimerization of two monolignols, which represents the entry point for the synthesis of 8-8′ lignans and contributes greatly to their structural diversity. Of particular interest has been in determining how differing substrate specificities are achieved with these enzymes. Here, we present crystal structures of IiPLR1/AtPrR1/AtPrR2 in the apo, substrate-binding and product-binding forms. Each structure contains a head-to-tail homodimer, and the catalytic pocket comprises structural elements from both monomers. A loop β4 covers the top of the pocket, and residue 98 from the loop governs catalytic specificity. Structure-guided mutagenesis could switch the substrate specificity of IiPLR1 and AtPrR2, respectively. Our study provides new insight into the molecular mechanism underlying the substrate specificity of PLR/PrRs and suggests an efficient strategy for the large-scale commercial production of the pharmaceutically valuable compound lariciresinol.

scholarly journals Structure-based engineering of substrate specificity for pinoresinol-lariciresinol reductases

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ying Xiao ◽  
Kai Shao ◽  
Jingwen Zhou ◽  
Lian Wang ◽  
Xueqi Ma ◽  
...  
Keyword(s):  
Substrate Specificity ◽  
Bound States ◽  
Large Scale ◽  
Structural Diversity ◽  
Structural Elements ◽  
Isatis Indigotica ◽  
Substrate Specificities ◽  
Lignan Biosynthesis ◽  
Insight Into

AbstractPinoresinol–lariciresinol reductases (PLRs) are enzymes involved in the lignan biosynthesis after the initial dimerization of two monolignols, and this represents the entry point for the synthesis of 8-8′ lignans and contributes greatly to their structural diversity. Of particular interest has been the determination of how differing substrate specificities are achieved with these enzymes. Here, we present crystal structures of IiPLR1 from Isatis indigotica and pinoresinol reductases (PrRs) AtPrR1 and AtPrR2 from Arabidopsis thaliana, in the apo, substrate-bound and product-bound states. Each structure contains a head-to-tail homodimer, and the catalytic pocket comprises structural elements from both monomers. β4 loop covers the top of the pocket, and residue 98 from the loop governs catalytic specificity. The substrate specificities of IiPLR1 and AtPrR2 can be switched via structure-guided mutagenesis. Our study provides insight into the molecular mechanism underlying the substrate specificity of PLRs/PrRs and suggests an efficient strategy for the large-scale commercial production of the pharmaceutically valuable compound lariciresinol.

scholarly journals Structural and evolutionary relationships of “AT-less” type I polyketide synthase ketosynthases

2015 ◽  
Vol 112 (41) ◽  
pp. 12693-12698 ◽  
Author(s):  
Jeremy R. Lohman ◽  
Ming Ma ◽  
Jerzy Osipiuk ◽  
Boguslaw Nocek ◽  
Youngchang Kim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Substrate Specificity ◽  
Polyketide Synthase ◽  
Acyl Carrier Protein ◽  
Structural Diversity ◽  
Type I ◽  
Substrate Specificities ◽  
In Trans ◽  
Canonical Type ◽  
Insight Into

Acyltransferase (AT)-less type I polyketide synthases (PKSs) break the type I PKS paradigm. They lack the integrated AT domains within their modules and instead use a discrete AT that acts in trans, whereas a type I PKS module minimally contains AT, acyl carrier protein (ACP), and ketosynthase (KS) domains. Structures of canonical type I PKS KS-AT didomains reveal structured linkers that connect the two domains. AT-less type I PKS KSs have remnants of these linkers, which have been hypothesized to be AT docking domains. Natural products produced by AT-less type I PKSs are very complex because of an increased representation of unique modifying domains. AT-less type I PKS KSs possess substrate specificity and fall into phylogenetic clades that correlate with their substrates, whereas canonical type I PKS KSs are monophyletic. We have solved crystal structures of seven AT-less type I PKS KS domains that represent various sequence clusters, revealing insight into the large structural and subtle amino acid residue differences that lead to unique active site topologies and substrate specificities. One set of structures represents a larger group of KS domains from both canonical and AT-less type I PKSs that accept amino acid-containing substrates. One structure has a partial AT-domain, revealing the structural consequences of a type I PKS KS evolving into an AT-less type I PKS KS. These structures highlight the structural diversity within the AT-less type I PKS KS family, and most important, provide a unique opportunity to study the molecular evolution of substrate specificity within the type I PKSs.

scholarly journals Sequence and Structural Analysis of AA9 and AA10 LPMOs: An Insight into the Basis of Substrate Specificity and Regioselectivity

2019 ◽  
Vol 20 (18) ◽  
pp. 4594 ◽  
Author(s):  
Xiaoli Zhou ◽  
Xiaohua Qi ◽  
Hongxia Huang ◽  
Honghui Zhu
Keyword(s):  
Structural Analysis ◽  
Substrate Specificity ◽  
Molecular Basis ◽  
Substrate Binding ◽  
Binding Modes ◽  
Substrate Specificities ◽  
Lytic Polysaccharide Monooxygenases ◽  
Polysaccharide Monooxygenases ◽  
Natural Carbon ◽  
Insight Into

Lytic polysaccharide monooxygenases (LPMOs) are key enzymes in both the natural carbon cycle and the biorefinery industry. Understanding the molecular basis of LPMOs acting on polysaccharide substrates is helpful for improving industrial cellulase cocktails. Here we analyzed the sequences, structures, and substrate binding modes of LPMOs to uncover the factors that influence substrate specificity and regioselectivity. Our results showed that the different compositions of a motif located on L2 affect the electrostatic potentials of substrate binding surfaces, which in turn affect substrate specificities of AA10 LPMOs. A conserved Asn at a distance of 7 Å from the active center Cu might, together with the conserved Ser immediately before the second catalytic His, determine the localization of LPMOs on substrate, and thus contribute to C4-oxidizing regioselectivity. The findings in this work provide an insight into the molecular basis of substrate specificity and regioselectivity of LPMOs.

scholarly journals Isoelectric focusing of glutathione S-transferases from rat liver and kidney

1978 ◽  
Vol 175 (3) ◽  
pp. 937-943 ◽  
Author(s):  
Barbara F. Hales ◽  
Valerie Jaeger ◽  
Allen H. Neims
Keyword(s):  
Substrate Specificity ◽  
Isoelectric Focusing ◽  
Transferase Activity ◽  
Sprague Dawley ◽  
Substrate Specificities ◽  
Liver Cytosol ◽  
Sprague Dawley Rats ◽  
Isoelectric Points ◽  
Liver And Kidney ◽  
Glutathione S Transferases

The glutathione S-transferases that were purified to homogeneity from liver cytosol have overlapping but distinct substrate specificities and different isoelectric points. This report explores the possibility of using preparative electrofocusing to compare the composition of the transferases in liver and kidney cytosol. Hepatic cytosol from adult male Sprague–Dawley rats was resolved by isoelectric focusing on Sephadex columns into five peaks of transferase activity, each with characteristic substrate specificity. The first four peaks of transferase activity (in order of decreasing basicity) are identified as transferases AA, B, A and C respectively, on the basis of substrate specificity, but the fifth peak (pI6.6) does not correspond to a previously described transferase. Isoelectric focusing of renal cytosol resolves only three major peaks of transferase activity, each with narrow substrate specificity. In the kidney, peak 1 (pI9.0) has most of the activity toward 1-chloro-2,4-dinitrobenzene, peak 2 (pI8.5) toward p-nitrobenzyl chloride, and peak 3 (pI7.0) toward trans-4-phenylbut-3-en-2-one. Renal transferase peak 1 (pI9.0) appears to correspond to transferase B on the basis of pI, substrate specificity and antigenicity. Kidney transferase peaks 2 (pI8.5) and 3 (pI7.0) do not correspond to previously described glutathione S-transferases, although kidney transferase peak 3 is similar to the transferase peak 5 from focused hepatic cytosol. Transferases A and C were not found in kidney cytosol, and transferase AA was detected in only one out of six replicates. Thus it is important to recognize the contribution of individual transferases to total transferase activity in that each transferase may be regulated independently.

scholarly journals Hierarchical mechanical metamaterials built with scalable tristable elements for ternary logic operation and amplitude modulation

2021 ◽  
Vol 7 (9) ◽  
pp. eabf1966
Author(s):  
Hang Zhang ◽  
Jun Wu ◽  
Daining Fang ◽  
Yihui Zhang
Keyword(s):  
Structural Diversity ◽  
Cell Number ◽  
Structural Elements ◽  
Ternary Logic ◽  
Stable States ◽  
One Dimensional ◽  
Logic Operation ◽  
Artificial Materials ◽  
Mechanical Metamaterials ◽  
Unit Cells

Multistable mechanical metamaterials are artificial materials whose microarchitectures offer more than two different stable configurations. Existing multistable mechanical metamaterials mainly rely on origami/kirigami-inspired designs, snap-through instability, and microstructured soft mechanisms, with mostly bistable fundamental unit cells. Scalable, tristable structural elements that can be built up to form mechanical metamaterials with an extremely large number of programmable stable configurations remains illusive. Here, we harness the elastic tensile/compressive asymmetry of kirigami microstructures to design a class of scalable X-shaped tristable structures. Using these structure as building block elements, hierarchical mechanical metamaterials with one-dimensional (1D) cylindrical geometries, 2D square lattices, and 3D cubic/octahedral lattices are designed and demonstrated, with capabilities of torsional multistability or independent controlled multidirectional multistability. The number of stable states increases exponentially with the cell number of mechanical metamaterials. The versatile multistability and structural diversity allow demonstrative applications in mechanical ternary logic operators and amplitude modulators with unusual functionalities.

scholarly journals Geo-Spatial Analysis of Population Density and Annual Income to Identify Large-Scale Socio-Demographic Disparities

2021 ◽  
Vol 10 (7) ◽  
pp. 432
Author(s):  
Nicolai Moos ◽  
Carsten Juergens ◽  
Andreas P. Redecker
Keyword(s):  
Population Density ◽  
Large Scale ◽  
Methodological Approach ◽  
Spatial Relationship ◽  
Postal Code ◽  
Annual Income ◽  
Choropleth Maps ◽  
Clustering Approach ◽  
Relationship Of ◽  
Insight Into

This paper describes a methodological approach that is able to analyse socio-demographic and -economic data in large-scale spatial detail. Based on the two variables, population density and annual income, one investigates the spatial relationship of these variables to identify locations of imbalance or disparities assisted by bivariate choropleth maps. The aim is to gain a deeper insight into spatial components of socioeconomic nexuses, such as the relationships between the two variables, especially for high-resolution spatial units. The used methodology is able to assist political decision-making, target group advertising in the field of geo-marketing and for the site searches of new shop locations, as well as further socioeconomic research and urban planning. The developed methodology was tested in a national case study in Germany and is easily transferrable to other countries with comparable datasets. The analysis was carried out utilising data about population density and average annual income linked to spatially referenced polygons of postal codes. These were disaggregated initially via a readapted three-class dasymetric mapping approach and allocated to large-scale city block polygons. Univariate and bivariate choropleth maps generated from the resulting datasets were then used to identify and compare spatial economic disparities for a study area in North Rhine-Westphalia (NRW), Germany. Subsequently, based on these variables, a multivariate clustering approach was conducted for a demonstration area in Dortmund. In the result, it was obvious that the spatially disaggregated data allow more detailed insight into spatial patterns of socioeconomic attributes than the coarser data related to postal code polygons.

Projects Selection and Evaluation Tools for the of Non-Conventional Materials and Technologies (NOCMATS)

2012 ◽  
Vol 517 ◽  
pp. 13-19 ◽  
Author(s):  
P. Ohayon ◽  
Khosrow Ghavami
Keyword(s):  
Large Scale ◽  
Evaluation Criteria ◽  
Second World War ◽  
Structural Elements ◽  
Industrialized Countries ◽  
Governmental Agencies ◽  
Vegetable Fibers ◽  
Private Organizations ◽  
The Social ◽  
Second World

The results of many successfully realized Research and Development (R&D) concerned with non-conventional materials and technologies (NOCMAT) in developing countries including Brazil have not been used in large scale in practice. This is due to the lack of selection and evaluation criteria and concepts from planning and designing to implementation programs by governmental agencies and private organizations concerned with the newly developed sustainable materials and technologies. The problems of selecting and evaluating R&D innovation outputs and impacts for construction are complex and need scientific and systematic studies in order to avoid the social and environmental mistakes occurred in industrialized countries after the Second World War. This paper presents a logical framework for the implementation of pertinent indicators to be used as a tool in R&D of NOCMAT projects selection and evaluation concerned with materials, structural elements and technologies of bamboo and composites reinforced with vegetable fibers. Indicators, related to the efficiency, effectiveness, impact, relevance and sustainability of such projects are considered and discussed.

Cytochrome P450 mono-oxygenases in conifer genomes: discovery of members of the terpenoid oxygenase superfamily in spruce and pine

2006 ◽  
Vol 34 (6) ◽  
pp. 1209-1214 ◽  
Author(s):  
B. Hamberger ◽  
J. Bohlmann
Keyword(s):  
Cytochrome P450 ◽  
Loblolly Pine ◽  
Large Scale ◽  
Expressed Sequence Tag ◽  
Resin Acid ◽  
Functional Characterization ◽  
Structural Diversity ◽  
Resin Acids ◽  
Full Length Sequence ◽  
Diterpene Resin Acids

Diterpene resin acids, together with monoterpenes and sesquiterpenes, are the most prominent defence chemicals in conifers. These compounds belong to the large group of structurally diverse terpenoids formed by enzymes known as terpenoid synthases. CYPs (cytochrome P450-dependent mono-oxygenases) can further increase the structural diversity of these terpenoids. While most terpenoids are characterized as specialized or secondary metabolites, some terpenoids, such as the phytohormones GA (gibberellic acid), BRs (brassinosteroids) and ABA (abscisic acid), have essential functions in plant growth and development. To date, very few CYP genes involved in conifer terpenoid metabolism have been functionally characterized and were limited to two systems, yew (Taxus) and loblolly pine (Pinus taeda). The characterized yew CYP genes are involved in taxol diterpene biosynthesis, while the only characterized pine terpenoid CYP gene is part of DRA (diterpene resin acid) biosynthesis. These CYPs from yew and pine are members of two apparently conifer-specific CYP families within the larger CYP85 clan, one of four plant CYP multifamily clans. Other CYP families within the CYP85 clan were characterized from a variety of angiosperms with functions in terpenoid phytohormone metabolism of GA, BR, and ABA. The recent development of EST (expressed sequence tag) and FLcDNA (where FL is full-length) sequence databases and cDNA collections for species of two conifers, spruce (Picea) and pine, allows for the discovery of new terpenoid CYPs in gymnosperms by means of large-scale sequence mining, phylogenetic analysis and functional characterization. Here, we present a snapshot of conifer CYP data mining, discovery of new conifer CYPs in all but one family within the CYP85 clan, and suggestions for their functional characterization. This paper will focus on the discovery of conifer CYPs associated with diterpene metabolism and CYP with possible functions in the formation of GA, BR, and ABA in conifers.

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