Structure and function of the thermostable L-asparaginase from Thermococcus kodakarensis.

L-Asparaginases catalyse the hydrolysis of asparagine to aspartic acid and ammonia. In addition, L-asparaginase is involved in the biosynthesis of amino acids such as lysine, methionine and threonine. These enzymes have been used as chemotherapeutic agents for the treatment of acute lymphoblastic leukaemia and other haematopoietic malignancies since the tumour cells cannot synthesize sufficient L-asparagine and are thus killed by deprivation of this amino acid. L-Asparaginases are also used in the food industry and have potential in the development of biosensors, for example for asparagine levels in leukaemia. The thermostable type I L-asparaginase from Thermococcus kodakarensis (TkA) is composed of 328 amino acids and forms homodimers in solution, with the highest catalytic activity being observed at pH 9.5 and 85°C. It has a Km value of 5.5 mM for L-asparagine, with no glutaminase activity being observed. The crystal structure of TkA has been determined at 2.18 Å resolution, confirming the presence of two α/β domains connected by a short linker region. The N-terminal domain contains a highly flexible β-hairpin which adopts `open' and `closed' conformations in different subunits of the solved TkA structure. In previously solved L-asparaginase structures this β-hairpin was only visible when in the `closed' conformation, whilst it is characterized with good electron density in all of the subunits of the TkA structure. A phosphate anion resides at the active site, which is formed by residues from both of the neighbouring monomers in the dimer. The high thermostability of TkA is attributed to the high arginine and salt-bridge content when compared with related mesophilic enzymes

Thermodynamic insights and assessment of the ‘circular economy’

This study analyses the effect on energy use of applying a wide range of circular economy approaches. By collating evidence on specific quantifiable approaches and then calculating and analyzing their combined full supply chain impacts through input-output analysis, it provides a more complete assessment of the overall potential scope for energy savings that these approaches might deliver than provided elsewhere. Assessment is conducted globally, across the EU-27 and in the UK. Overall, the identified opportunities have the potential to save 6%–11% of energy used to support economic activity, worldwide and in the EU, and 5%–8% in the UK. Their potential is equivalent to the total scope for other industrial energy efficiency savings. The potential savings are further divided into those due to sets of approaches relating to food waste, steel production, other materials production, product refurbishment, vehicle provision, construction and other equipment manufacture. Each of these sets of approaches can make a key contribution to the total savings that are possible. Complementary use of energy and exergy metrics illustrates the way in which energy use might change and for the first time provides indication that in most cases other energy efficiency measures are unlikely to be adversely affected by the circular economy approaches. Potential for savings in the energy embodied in each key product input to each major sector is assessed, enabling prioritization of the areas in which the circular economy approaches have the greatest scope for impact and identification of supply chains for which they are underrepresented

Structure of the 2,4'-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP.

The enzyme 2,4'-dihydroxyacetophenone dioxygenase (DAD) catalyses the conversion of 2,4'-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid with the incorporation of molecular oxygen. Whilst the vast majority of dioxygenases cleave within the aromatic ring of the substrate, DAD is very unusual in that it is involved in C-C bond cleavage in a substituent of the aromatic ring. There is evidence that the enzyme is a homotetramer of 20.3 kDa subunits, each containing nonhaem iron, and its sequence suggests that it belongs to the cupin family of dioxygenases. In this paper, the first X-ray structure of a DAD enzyme from the Gram-negative bacterium Alcaligenes sp. 4HAP is reported, at a resolution of 2.2 Å. The structure establishes that the enzyme adopts a cupin fold, forming dimers with a pronounced hydrophobic interface between the monomers. The catalytic iron is coordinated by three histidine residues (76, 78 and 114) within a buried active-site cavity. The iron also appears to be tightly coordinated by an additional ligand which was putatively assigned as a carbonate dianion since this fits the electron density optimally, although it might also be the product formate. The modelled carbonate is located in a position which is highly likely to be occupied by the α-hydroxyketone group of the bound substrate during catalysis. Modelling of a substrate molecule in this position indicates that it will interact with many conserved amino acids in the predominantly hydrophobic active-site pocket where it undergoes peroxide radical-mediated heterolysis

Stellar mass function of cluster galaxies at z ~ 1.5: evidence for reduced quenching efficiency at high redshift

Indexación: Web of ScienceWe present the stellar mass functions (SMFs) of passive and star-forming galaxies with a limiting mass of 10(10.1) M-circle dot in four spectroscopically confirmed Spitzer Adaptation of the Red-sequence Cluster Survey (SpARCS) galaxy clusters at 1 : 37 < z < 1 : 63. The clusters have 113 spectroscopically confirmed members combined, with 8-45 confirmed members each. We construct Ks-bandselected photometric catalogs for each cluster with an average of 11 photometric bands ranging from u to 8 mu m. We compare our cluster galaxies to a field sample derived from a similar Ks-band-selected catalog in the UltraVISTA / COSMOS field. The SMFs resemble those of the field, but with signs of environmental quenching. We find that 30 +/- 20% of galaxies that would normally be forming stars in the field are quenched in the clusters. The environmental quenching e ffi ciency shows little dependence on projected cluster-centric distance out to similar to 4 Mpc, providing tentative evidence of pre-processing and/or galactic conformity in this redshift range. We also compile the available data on environmental quenching efficiencies from the literature, and find that the quenching e ffi ciency in clusters and in groups appears to decline with increasing redshift in a manner consistent with previous results and expectations based on halo mass growth.http://www.aanda.org/articles/aa/abs/2016/08/aa28663-16/aa28663-16.htm

Irreversible reorganization in a supercooled liquid originates from localised soft modes

The transition of a fluid to a rigid glass upon cooling is a common route of transformation from liquid to solid that embodies the most poorly understood features of both phases1,2,3. From the liquid perspective, the puzzle is to understand stress relaxation in the disordered state. From the perspective of solids, the challenge is to extend our description of structure and its mechanical consequences to materials without long range order. Using computer simulations, we show that the localized low frequency normal modes of a configuration in a supercooled liquid are causally correlated to the irreversible structural reorganization of the particles within that configuration. We also demonstrate that the spatial distribution of these soft local modes can persist in spite of significant particle reorganization. The consequence of these two results is that it is now feasible to construct a theory of relaxation length scales in glass-forming liquids without recourse to dynamics and to explicitly relate molecular properties to their collective relaxation.Comment: Published online: 20 July 2008 | doi:10.1038/nphys1025 Available from http://www.nature.com/nphys/journal/v4/n9/abs/nphys1025.htm

Structure and function of the type III pullulan hydrolase from Thermococcus kodakarensis

Pullulan-hydrolysing enzymes, more commonly known as debranching enzymes for starch and other polysaccharides, are of great interest and have been widely used in the starch-saccharification industry. Type III pullulan hydrolase from Thermococcus kodakarensis (TK-PUL) possesses both pullulanase and α-amylase activities. Until now, only two enzymes in this class, which are capable of hydrolysing both α-1,4- and α-1,6-glycosidic bonds in pullulan to produce a mixture of maltose, panose and maltotriose, have been described. TK-PUL shows highest activity in the temperature range 95–100°C and has a pH optimum in the range 3.5–4.2. Its unique ability to hydrolyse maltotriose into maltose and glucose has not been reported for other homologous enzymes. The crystal structure of TK-PUL has been determined at a resolution of 2.8 Å and represents the first analysis of a type III pullulan hydrolyse. The structure reveals that the last part of the N-terminal domain and the C-terminal domain are significantly different from homologous structures. In addition, the loop regions at the active-site end of the central catalytic domain are quite different. The enzyme has a well defined calcium-binding site and possesses a rare vicinal disulfide bridge. The thermostability of TK-PUL and its homologues may be attributable to several factors, including the increased content of salt bridges, helical segments, Pro, Arg and Tyr residues and the decreased content of serine

Thermodynamic insights and assessment of the ‘circular economy’

This study analyses the effect on energy use of applying a wide range of circular economy approaches. By collating evidence on specific quantifiable approaches and then calculating and analyzing their combined full supply chain impacts through input-output analysis, it provides a more complete assessment of the overall potential scope for energy savings that these approaches might deliver than provided elsewhere. Assessment is conducted globally, across the EU-27 and in the UK. Overall, the identified opportunities have the potential to save 6%–11% of energy used to support economic activity, worldwide and in the EU, and 5%–8% in the UK. Their potential is equivalent to the total scope for other industrial energy efficiency savings. The potential savings are further divided into those due to sets of approaches relating to food waste, steel production, other materials production, product refurbishment, vehicle provision, construction and other equipment manufacture. Each of these sets of approaches can make a key contribution to the total savings that are possible. Complementary use of energy and exergy metrics illustrates the way in which energy use might change and for the first time provides indication that in most cases other energy efficiency measures are unlikely to be adversely affected by the circular economy approaches. Potential for savings in the energy embodied in each key product input to each major sector is assessed, enabling prioritization of the areas in which the circular economy approaches have the greatest scope for impact and identification of supply chains for which they are underrepresented

The 1.1 angstrom resolution structure of a periplasmic phosphate-binding protein from Stenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank

During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from Alcaligenes sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this new structure as the search model did not give a convincing solution with the original atomic resolution data set. Hence, it was considered that these crystals might have arisen from a protein impurity, although molecular replacement using the structures of common crystallization contaminants as search models again failed. A script to perform molecular replacement using MOLREP in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate-binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron-density map at 1.1 Å resolution based on the solution obtained with PDB entry 2q9t allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate-binding protein from Stenotrophomonas maltophilia (UniProt ID B4SL31; gene ID Smal_2208), and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked to the virulence of antibiotic-resistant strains of pathogenic bacteria and with biofilm formation. The structure of the S. maltophilia protein has been refined to an R factor of 10.15% and an Rfree of 12.46% at 1.1 Å resolution. The molecule adopts the type II periplasmic binding protein (PBP) fold with a number of extensively elaborated loop regions. A fully dehydrated phosphate anion is bound tightly between the two domains of the protein and interacts with conserved residues and a number of helix dipoles