A5060858412- Microbial bioremediation and biosurfactants
- Enzyme Structure and Function
- Microbial metabolism and enzyme function
- Microbial Metabolic Engineering and Bioproduction
- Enzyme Catalysis and Immobilization
- RNA and protein synthesis mechanisms
- Protein Structure and Dynamics
- Macrophage Migration Inhibitory Factor
- Plant biochemistry and biosynthesis
- Pharmacogenetics and Drug Metabolism
- Enzyme Production and Characterization
- Microbial Natural Products and Biosynthesis
- Biochemical and Molecular Research
- Fungal and yeast genetics research
- Biofuel production and bioconversion
- Mass Spectrometry Techniques and Applications
- Chemical Reactions and Isotopes
- Pancreatic function and diabetes
- Bacterial Genetics and Biotechnology
- Health Systems, Economic Evaluations, Quality of Life
- Glycosylation and Glycoproteins Research
- Peptidase Inhibition and Analysis
- Steroid Chemistry and Biochemistry
- Amino Acid Enzymes and Metabolism
- Photosynthetic Processes and Mechanisms
DSM (Netherlands)
2013-2023
Columbia University
2007
University of Groningen
2001-2006
NOAA Chemical Sciences Laboratory
2006
Summary N ootkatone is one of the major terpenes in heartwood ootka cypress C allitropsis nootkatensis . It an oxidized sesquiterpene, which has been postulated to be derived from valencene. Both valencene and nootkatone are used for flavouring citrus beverages considered among most valuable at commercial scale. Functional evaluation putative terpene synthase genes sourced by large‐scale EST sequencing wood revealed a gene ( n VS ) expression different tissues tree correlates well with...
Engineering of Saccharomyces cerevisiae for the simultaneous utilization hexose and pentose sugars is vital cost-efficient cellulosic bioethanol production. This yeast lacks specific transporters depends on endogenous low affinity uptake. Consequently, engineered xylose-fermenting strains first utilize D-glucose before D-xylose can be transported metabolized. We have used an evolutionary engineering approach that a quadruple hexokinase deletion S. strain to select growth in presence high...
Interactions between small molecules and proteins play critical roles in regulating facilitating diverse biological functions, yet our ability to accurately re-engineer the specificity of these interactions using computational approaches has been limited. One main difficulty, addition inaccuracies energy is exquisite sensitivity protein–ligand subtle conformational changes, coupled with problem sampling large search space degrees freedom ligands, amino acid side chains, protein backbone....
The yeast Saccharomyces cerevisiae is unable to ferment pentose sugars like d-xylose. Through the introduction of respective metabolic pathway, S. able xylose but first utilizes d-glucose before d-xylose can be transported and metabolized. Low affinity uptake occurs through endogenous hexose (Hxt) transporters. For a more robust sugar fermentation, co-consumption desired as fermentation in particular prone inhibition by compounds present pretreated lignocellulosic feedstocks.Evolutionary...
(+)‐Nootkatone is a natural sesquiterpene ketone used in grapefruit and citrus flavour compositions. It occurs small amounts major component of Alaska cedar ( Callitropsis nootkatensis ) heartwood essential oil. Upon co‐expression candidate cytochrome P450 enzymes from yeast with valencene synthase, C. oxidase (CnVO) was identified to produce trans ‐nootkatol (+)‐nootkatone. Formation (+)‐nootkatone detected at 144 ± 10 μg/L culture. CnVO belongs new subfamily the CYP706 family oxidases.
Halo alcohol dehalogenase HheC catalyzes the highly enantioselective dehalogenation of vicinal halo alcohols to epoxides, as well reverse reaction, and β-regioselective nucleophilic ring opening epoxides by pseudo-halides such azide cyanide. To investigate this latter we determined X-ray structures complexes with favored unfavored enantiomers para-nitrostyrene oxide. The aromatic parts two bind in a very similar way, but epoxide (S)-enantiomer binds nonproductive inverted manner, oxygen Cβ...
Xylose isomerase from Piromyces sp. E2 (PirXI) can be used to equip Saccharomyces cerevisiae with the capacity ferment xylose ethanol. The biochemical properties and structure of enzyme have not been described even though its metal content, catalytic parameters, expression level are critical for rapid utilization. We isolated after high-level in Escherichia coli, analyzed dependence properties, determined 12 crystal structures presence different metals, substrates, substrate analogues....
Halohydrin dehalogenase (HheC) from Agrobacterium radiobacter AD1 catalyzes the dehalogenation of vicinal haloalcohols by an intramolecular substitution reaction, resulting in formation corresponding epoxide, a halide ion, and proton. Halide release is rate-limiting during catalytic cycle conversion (R)-p-nitro-2-bromo-1-phenylethanol enzyme. The recent elucidation X-ray structure HheC showed that hydrogen bonds between OH group Tyr187 Oδ1 atom Asn176 Nε1 Trp249 could play role stabilizing...
Proline-specific endoproteases have been successfully used in, for example, the in-situ degradation of gluten, hydrolysis bitter peptides, reduction haze during beer production, and generation peptides mass spectroscopy proteomics applications. Here we present crystal structure extracellular proline-specific endoprotease from Aspergillus niger (AnPEP), a member S28 peptidase family with rarely observed true activity. Family proteases conventional Ser-Asp-His catalytic triad, but their...
The bacterial degradation pathways for the nematocide 1,3-dichloropropene rely on hydrolytic dehalogenation reactions catalyzed by cis- and trans-3-chloroacrylic acid dehalogenases (cis-CaaD CaaD, respectively). X-ray crystal structures of native cis-CaaD inactivated (R)-oxirane-2-carboxylate were elucidated. They locate four known catalytic residues (Pro-1, Arg-70, Arg-73, Glu-114) two previously unknown, potential (His-28 Tyr-103'). Y103F H28A mutants these latter displayed reductions in...
Haloalcohol dehalogenases are bacterial enzymes that cleave the carbon-halogen bond in short aliphatic vicinal haloalcohols, like 1-chloro-2,3-propanediol, some of which recalcitrant environmental pollutants. They use a conserved Ser-Tyr-Arg catalytic triad to deprotonate haloalcohol oxygen, attacks halogen-bearing carbon atom, producing an epoxide and halide ion. Here, we present X-ray structure dehalogenase HheA(AD2) from Arthrobacter sp. strain AD2 at 2.0-A resolution. Comparison with...
CYP105AS1 is a cytochrome P450 from Amycolatopsis orientalis that catalyzes monooxygenation of compactin to 6-epi-pravastatin. For fermentative production the cholesterol-lowering drug pravastatin, stereoselectivity enzyme needs be inverted, which has been partially achieved by error-prone PCR mutagenesis and screening. In current study, we report further optimization computationally aided approach. Using CoupledMoves protocol Rosetta, virtual library mutants was designed bind in...
CorNet is a web-based tool for the analysis of co-evolving residue positions in protein super-family sequence alignments. projects external information such as mutation data extracted from literature on interactively displayed groups to shed light functions associated with these and residues them. We used analyse six enzyme super-families found that strongly tend consist involved same function activity, specificity, co-factor binding, or enantioselectivity. This finding allows assign which...
Rhodoxanthin is a vibrant red carotenoid found across the plant kingdom and in certain birds fish. It member of atypical retro class carotenoids, which contain an additional double bond concerted shift conjugated bonds relative to more widely occurring pigments, whose biosynthetic origins have long remained elusive. Here, we identify LHRS (Lonicera hydroxylase rhodoxanthin synthase), variant β-carotene (BCH)-type integral membrane diiron enzyme that mediates conversion into rhodoxanthin. We...
Halohydrin dehalogenases are key enzymes in the bacterial degradation of vicinal halopropanols and structurally related nematocides. Crystals enantioselective halohydrin dehalogenase HheC from Agrobacterium radiobacter AD1 have been obtained at room temperature hanging-drop vapour-diffusion experiments against 50-70% saturated ammonium sulfate solution pH 6.5-7.3. The crystals belong to space group P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters a = b 104.5, c 121.4 A, contain two...
Deazaflavin-dependent whole-cell conversions in well-studied and industrially relevant microorganisms such as Escherichia coli Saccharomyces cerevisiae have high potential for the biocatalytic production of valuable compounds. The artificial deazaflavin FOP (FO-5′-phosphate) can functionally substitute natural F420 be synthesized fewer steps, offering a solution to limited availability latter due its complex (bio)synthesis. Herein we set out produce vivo scalable method means FOP-mediated...
Crystals were grown of a mutant form the bacterial cell-wall maintenance protein MltA that diffracted to 2.15 A resolution. When phasing with molecular replacement using native structure failed, selenium MAD was used obtain initial phases. However, after crystals found be tetartohedrally twinned, hampering correct space-group determination and refinement. refinement protocol designed take tetartohedral twinning into account successfully applied refine structure. The is described reasons for...
In class C beta-lactamases, the strictly conserved Asn152 forms part of an extended active-site hydrogen-bonding network. To probe its role in catalysis, all 19 mutants Enterobacter cloacae P99 cephalosporinase were simultaneously constructed and screened Escherichia coli for their vivo activity. The screen identified previously uncharacterized Asn152Ser, Asn152Thr, Asn152Gly, which possess significant activity altered substrate selectivity. vitro measurement Michaelis-Menten kinetic...