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At least 19 records

Patient mutations in human ATP:cob(I)alamin adenosyltransferase differentially affect its catalytic versus chaperone functions

Human ATP:cob(I)alamin adenosyltransferase (ATR) is a mitochondrial enzyme that catalyzes an adenosyl transfer to cob(I)alamin, synthesizing 5'-deoxyadenosylcobalamin (AdoCbl) or coenzyme B 12 . ATR is also a chaperone that escorts AdoCbl, transferring it to methylmalonyl-CoA mutase, which is important in propionate metabolism. Mutations in ATR lead to methylmalonic aciduria type B, an inborn error of B12 metabolism. Our previous studies have furnished insights into how ATR protein dynamics influence redox-linked cobalt coordination chemistry, controlling its catalytic versus chaperone functions. In this study, we have characterized three patient mutations at two conserved active site residues in human ATR, R190C/H, and E193K and obtained crystal structures of R190C and E193K variants, which display only subtle structural changes. All three mutations were found to weaken affinities for the cob(II)alamin substrate and the AdoCbl product and increase K M(ATP) . 31 P NMR studies show that binding of the triphosphate product, formed during the adenosylation reaction, is also weakened. However, although the k cat of this reaction is significantly diminished for the R190C/H mutants, it is comparable with the WT enzyme for the E193K variant, revealing the catalytic importance of Arg-190. Furthermore, although the E193K mutation selectively impairs the chaperone function by promoting product release into solution, its catalytic function might be unaffected at physiological ATP concentrations. In contrast, the R190C/H mutations affect both the catalytic and chaperoning activities of ATR. Because the E193K mutation spares the catalytic activity of ATR, our data suggest that the patients carrying this mutation are more likely to be responsive to cobalamin therapy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED

ABSTRACT Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that the reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by Methanosarcina acetivorans . In order to gain insight into how the cells sense and respond to the availability of the terminal electron acceptor, we designed an experiment to deplete cells of the essential terminal oxidase enzyme, HdrED. We found that the depletion of HdrED in vivo results in a higher abundance of transcripts for methyltransferases ( mtaC2, mtaB3, mtaC3 ), coenzyme B biosynthesis, C1 metabolism, and pyrimidine compounds. In most cases, these changes were distinct from transcript abundance changes observed during the transition from exponential growth to stationary phase cultures. These data implicate the methylotrophic methanogenesis regulator MsrC (MA4383) in CoM-S-S-CoB heterodisulfide sensing and indicate cells have a specific mechanism to sense intracellular ratio of CoM-S-S-CoB, coenzyme M, and coenzyme B thiols and further suggest transcripts encoding translation and methanogenesis functions are controlled by feed-forward regulation depending on substrate availability. IMPORTANCE Methanosarcina is an emerging model archaeon and synthetic biology platform for the production of renewable energy and sustainable chemicals to reduce dependence on petroleum. Research into metabolic networks and gene regulation in this organism and other methanogens will inform genome-scale metabolic modeling and microbial function prediction in uncultured or non-model anaerobes and archaea. This study suggests methanogens use unknown mechanisms to efficiently couple methanogenesis to gene regulation via CoM-S-S-CoB and ATP availability.

Buan, Nicole R. (ORCID:000000027560973X)↗

Yield stress and flow behavior of enzyme liquefied slurries from corn cobs and corn stover pellets

With the increase in population, the world will depend on renewable sources to meet the increasing energy needs. The use of lignocellulosic biomass as a renewable source has been proven efficient for conversion to cellulosic ethanol and capable of contributing to thresholds for energy demand while reducing greenhouse gases by 90% when compared with fossil fuels. However, limitations in feeding and flow within biorefineries is encountered when system plugging occurs due to biomass compaction and a high yield stress for slurries formed during its processing, thereby preventing transport of biomass materials between plant unit operations. In some cases, this leads to unexpected plant shutdowns increasing industrial operational costs. As an alternative, enzyme-assisted liquefaction for slurry creation from corn stover at solids loadings up to 30% is reported in this work. Two different kinds of biomass (pelleted corn stover and cobs) were liquefied in a fed-batch process using commercial enzymes Celluclast 1.5L or Ctec-2 at 1FPU or 3 FPU per gram of dry solids in 10 mM sodium citrate buffer solution (pH 4.8). Pellets were fed into a 1 L stirred bioreactor according to a pre-defined fed-batch protocol over the first 5 hours until reaching 30% of solids loading. After 6, 24 and 96 hours, samples were taken and characterized with respect to their sugar composition, rheology and water absorption. Successful slurry creation with dramatically reduced yield stress was achieved for corn stover for both assessed enzymes. Yield stresses of 178±7 Pa (3 FPU, Celluclast 1.5L) and 79±6 Pa (3 FPU, Ctec-2) were measured for corn stover at 24 hours, compared to 6,000 Pa for samples without enzyme. Yield stress was 155± 29 Pa (3FPU, Ctec-2) and 257 ± 72 Pa (1 FPU,Celluclast 1.5L) for corn cobs at 24 hours. Yield stress decreased when residence time increased with an enhanced fluidity noted for higher enzyme concentrations. A profile for 6, 24 and 96h of yield stress measurements is presented.

Guitierrez, Diana↗

Materials Data on CoB by Materials Project

CoB crystallizes in the orthorhombic Pnma space group. The structure is three-dimensional. Co3+ is bonded in a 7-coordinate geometry to seven equivalent B3- atoms. There are a spread of Co–B bond distances ranging from 2.08–2.15 Å. B3- is bonded in a 9-coordinate geometry to seven equivalent Co3+ and two equivalent B3- atoms. Both B–B bond lengths are 1.84 Å.

36 MATERIALS SCIENCE↗

Materials Data on U(CoB)4 by Materials Project

U(CoB)4 crystallizes in the tetragonal P4_2/nmc space group. The structure is three-dimensional. U4+ is bonded in a 12-coordinate geometry to twelve equivalent B3- atoms. There are eight shorter (2.86 Å) and four longer (2.91 Å) U–B bond lengths. Co2+ is bonded in a 5-coordinate geometry to five equivalent B3- atoms. There are four shorter (2.07 Å) and one longer (2.10 Å) Co–B bond lengths. B3- is bonded in a 6-coordinate geometry to three equivalent U4+, five equivalent Co2+, and one B3- atom. The B–B bond length is 1.74 Å.

36 MATERIALS SCIENCE↗

Materials Data on Er(CoB)2 by Materials Project

Er(CoB)2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Er3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Er–B bond lengths are 2.84 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of corner and edge-sharing CoB4 tetrahedra. All Co–B bond lengths are 2.01 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Er3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on La(CoB)4 by Materials Project

La(CoB)4 crystallizes in the tetragonal P4_2/n space group. The structure is three-dimensional. La3+ is bonded in a 12-coordinate geometry to twelve equivalent B3- atoms. There are a spread of La–B bond distances ranging from 2.82–3.31 Å. Co+2.25+ is bonded in a 5-coordinate geometry to five equivalent B3- atoms. There are a spread of Co–B bond distances ranging from 2.00–2.52 Å. B3- is bonded in a 5-coordinate geometry to three equivalent La3+, five equivalent Co+2.25+, and one B3- atom. The B–B bond length is 1.81 Å.

36 MATERIALS SCIENCE↗

Materials Data on GdY(CoB)4 by Materials Project

GdY(CoB)4 crystallizes in the tetragonal P4/mmm space group. The structure is three-dimensional. Gd3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Gd–B bond lengths are 2.91 Å. Y3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Y–B bond lengths are 2.89 Å. Co+1.50+ is bonded to four B3- atoms to form a mixture of edge and corner-sharing CoB4 tetrahedra. All Co–B bond lengths are 2.01 Å. There are two inequivalent B3- sites. In the first B3- site, B3- is bonded in a 4-coordinate geometry to four equivalent Gd3+ and four equivalent Co+1.50+ atoms. In the second B3- site, B3- is bonded in a 4-coordinate geometry to four equivalent Y3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Cob Control

Python scripts for parallel-controlling RCE's on a SLAC COB.

Cheong, Sanha↗

Liquefaction of pelleted corn cobs

Liquid slurries at high loadings (pumpable slurries) are critical to handle the streams between the unit operations in a biorefinery. Their liquefaction potential was initially tested with a small-scale method using 3FPU Ctec-2 /g dry biomass, and results were confirmed in 1L bioreactors experiments. Liquid slurries of cobs were observed in small scale tests (based on visual appearance, and reducing sugars released). Results were confirmed in 1L bioreactors under similar experimental conditions. Yield stress value in bioreactor was 34 ± 6Pa at 96 h, and glucan and xylan conversion to glucose and xylose, respectively, were 41 and 21%. In addition, work has been initiated with liquefaction of other pelleted corn stover fractions: Husk/Leaf (A),Husk (B), Stems (D) and controls (whole corn stover; F and G). Compositional analysis of the pellets showed glucan content (%) in the samples ranged from 31.9 to 36.1, xylan from 19.1 to 20.9, total lignin 13.1 to 18.8,and total ash 1.73 to 10.19. The moisture content ranged from 6.21 to 11.66%. Given these similar characteristics, we also examined liquefaction of these other samples, and they also showed that liquid slurries are possible. Work is continuing to define favourable conditions for liquid slurries formation.

Cruz, Antonio↗

Materials Data on La(CoB)2 by Materials Project

LaCo2B2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. La3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All La–B bond lengths are 3.07 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of distorted corner and edge-sharing CoB4 tetrahedra. All Co–B bond lengths are 1.99 Å. B3- is bonded in a 4-coordinate geometry to four equivalent La3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on Y(CoB)2 by Materials Project

YCo2B2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Y3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Y–B bond lengths are 2.89 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of distorted edge and corner-sharing CoB4 tetrahedra. All Co–B bond lengths are 2.00 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Y3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on Tb(CoB)2 by Materials Project

TbCo2B2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Tb3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Tb–B bond lengths are 2.90 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of distorted corner and edge-sharing CoB4 tetrahedra. All Co–B bond lengths are 2.00 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Tb3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on Sm(CoB)2 by Materials Project

SmCo2B2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Sm3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Sm–B bond lengths are 2.96 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of distorted corner and edge-sharing CoB4 tetrahedra. All Co–B bond lengths are 2.00 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Sm3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on Pr(CoB)2 by Materials Project

PrCo2B2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Pr3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Pr–B bond lengths are 3.03 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of distorted edge and corner-sharing CoB4 tetrahedra. All Co–B bond lengths are 1.99 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Pr3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on Dy(CoB)2 by Materials Project

DyCo2B2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Dy3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Dy–B bond lengths are 2.88 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of distorted edge and corner-sharing CoB4 tetrahedra. All Co–B bond lengths are 2.00 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Dy3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on Nd(CoB)2 by Materials Project

NdCo2B2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Nd3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Nd–B bond lengths are 3.01 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of distorted edge and corner-sharing CoB4 tetrahedra. All Co–B bond lengths are 1.99 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Nd3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗

Materials Data on Ho(CoB)2 by Materials Project

HoCo2B2 crystallizes in the tetragonal I4/mmm space group. The structure is three-dimensional. Ho3+ is bonded in a body-centered cubic geometry to eight equivalent B3- atoms. All Ho–B bond lengths are 2.87 Å. Co+1.50+ is bonded to four equivalent B3- atoms to form a mixture of edge and corner-sharing CoB4 tetrahedra. All Co–B bond lengths are 2.01 Å. B3- is bonded in a 4-coordinate geometry to four equivalent Ho3+ and four equivalent Co+1.50+ atoms.

36 MATERIALS SCIENCE↗