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We have developed a system for producing a supramolecular scaffold that permeates the entire Escherichia coli cytoplasm. This cytoscaffold is constructed from a three-component system comprising a bacterial microcompartment shell protein and two complementary de novo coiled-coil peptides. We show that other proteins can be targeted to this intracellular filamentous arrangement. Specifically, the enzymes pyruvate decarboxylase and alcohol dehydrogenase have been directed to the filaments, leading to enhanced ethanol production in these engineered bacterial cells compared to those that do not produce the scaffold. This is consistent with improved metabolic efficiency through enzyme colocation. Finally, the shell-protein scaffold can be directed to the inner membrane of the cell, demonstrating how synthetic cellular organization can be coupled with spatial optimization through in-cell protein design. The cytoscaffold has potential in the development of next-generation cell factories, wherein it ...

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Homologous recombination (HR) is essential for the accurate repair of DNA double-strand breaks (DSBs), potentially lethal lesions. HR takes place in the late S-G2 phase of the cell cycle and involves the generation of a single-stranded region of DNA, followed by strand invasion, formation of a Holliday junction, DNA synthesis using the intact strand as a template, branch migration and resolution. It is investigated that RecA/Rad51 family proteins play a central role. The breast cancer susceptibility protein Brca2 and the RecQ helicase BLM (Bloom syndrome mutated) are tumor suppressors that maintain genome integrity, at least in part, through HR ...

p,The ethanolamine utilization (Eut) microcompartment is a protein-based metabolic organelle that is strongly associated with pathogenesis in bacteria that inhabit the human gut. The exterior shell of this elaborate protein complex is composed from a few thousand copies of BMC-domain shell proteins, which form a semi-permeable diffusion barrier that provides the interior enzymes with substrates and cofactors while simultaneously retaining metabolic intermediates. The ability of this protein shell to regulate passage of substrate and cofactor molecules is critical for microcompartment function, but the details of how this diffusion barrier can allow the passage of large cofactors while still retaining small intermediates remain unclear. Previous work has revealed two conformations of the EutL shell protein, providing substantial evidence for a gated pore that might allow the passage of large cofactors. Here we report structural and biophysical evidence to show that ethanolamine, the substrate of ...

Synthesis gas, a mixture of CO, H2, and CO2, is a promising renewable feedstock for bio-based production of organic chemicals. Production of medium-chain fatty acids can be performed via chain elongation, utilizing acetate and ethanol as main substrates. Acetate and ethanol are main products of syngas fermentation by acetogens. Therefore, syngas can be indirectly used as a substrate for the chain elongation process. Here, we report the establishment of a synthetic co-culture consisting of Clostridium autoethanogenum and Clostridium kluyveri. Together, these bacteria are capable of converting CO and syngas to a mixture of C4 and C6 fatty acids and their respective alcohols. The co-culture is able to grow using solely CO or syngas as a substrate, and presence of acetate significantly stimulated production rates. The co-culture produced butyrate and caproate at a rate of 8.5 ± 1.1 and 2.5 ± 0.63 mmol/l/day, respectively. Butanol and hexanol were produced at a rate of 3.5 ± 0.69 and 2.0 ± 0.46 mmol/l

Enzymes participating in ethanol utilization and catabolism. Each row of panels shows the expression levels of a set of enzymes catalyzing a reaction from ethan

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Encapsulins are a large and widely distributed family of proteins and are present in most bacteria and have been identified in Candidatus methanoregula, a species of archaea. They were originally called linocin-like proteins and thought to be a group of bacterial antibiotics, since they showed bacteriostatic activity in culture. However, structural analysis showed these to form a spherical nanocompartment that contains enzymes involved in the defenses against oxidative stress.[3] ...

This study was designed to achieve better understanding of (1) how carboxysome genes are regulated and expressed to yield with precise relative ratios and (2) the in vivo roles of two sets of conserved bacterial microcompartment genes, namely the three csoS1 and two csoS4 genes of H. neapolitanus , in the biogenesis and function of the carboxysome. For the first goal, a detailed transcriptional profile of carboxysomal genes in H. neapolitanus was established using absolute quantification real-time RT-PCR and transcript ends analysis. This transcriptional profile revealed that a single promoter, denoted cso promoter, was located upstream from the clustered carboxysomal genes. Transcripts of all nine carboxysomal genes were detectable but were present at different levels. In vivo activities of the cso promoter and selected internal non-coding regions within the carboxysome operon were further examined by using a promoter reporter vector and by generating a cso promoter deletion mutant. Both

AE006468.LEUA Location/Qualifiers FT CDS_pept complement(132167..133738) FT /codon_start=1 FT /transl_table=11 FT /gene=leuA FT /locus_tag=STM0113 FT /product=2-isopropylmalate synthase FT /EC_number=2.3.3.13 FT /note=similar to E. coli 2-isopropylmalate synthase FT (AAC73185.1); Blastp hit to AAC73185.1 (523 aa), 92% FT identity in aa 1 - 523 FT /db_xref=EnsemblGenomes-Gn:STM0113 FT /db_xref=EnsemblGenomes-Tr:AAL19077 FT /db_xref=GOA:P15875 FT /db_xref=InterPro:IPR000891 FT /db_xref=InterPro:IPR002034 FT /db_xref=InterPro:IPR005671 FT /db_xref=InterPro:IPR013709 FT /db_xref=InterPro:IPR013785 FT /db_xref=InterPro:IPR036230 FT /db_xref=UniProtKB/Swiss-Prot:P15875 FT /protein_id=AAL19077.1 FT /translation=MSQQVIIFDTTLRDGEQALQASLSAKEKLQIALALERMGVDVMEV FT GFPVSSPGDFESVQTIARTIKNSRVCALARCVEKDIDVAAQALKVADAFRIHTFIATSP FT MHIATKLRSTLDEVIERAVYMVKRARNYTDDVEFSCEDAGRTPVDDLARVVEAAINAGA FT RTINIPDTVGYTMPFEFAGIISGLYERVPNIDKAIISVHTHDDLGIAVGNSLAAVHAGA FT ...

Immobilization of two organometallic complexes into a single cage to construct protein-based microcompartmentImmobilization of two organometallic complexes into a single cage to construct protein-based microcompartment ...

InterPro provides functional analysis of proteins by classifying them into families and predicting domains and important sites. We combine protein signatures from a number of member databases into a single searchable resource, capitalising on their individual strengths to produce a powerful integrated database and diagnostic tool.

TY - JOUR. T1 - Downregulation of dihydrolipoyl dehydrogenase by UVA suppresses melanoma progression via triggering oxidative stress and altering energy metabolism. AU - Yumnam, Silvia. AU - Kang, Min Cheol. AU - Oh, Seung Hyun. AU - Kwon, Hak Cheol. AU - Kim, Jin Chul. AU - Jung, Eun Sung. AU - Lee, Choong Hwan. AU - Lee, Ai Young. AU - Hwang, Jong Ik. AU - Kim, Sun Yeou. N1 - Funding Information: This work was supported by the KIST Institutional Program (Project No. 2E29563-19-120 ) and Ambrobnp (Seoul, Korea), grant number 202006250001. We would like to thank Editage ( www.editage.co.kr ) for English language editing. Publisher Copyright: © 2020 The Author(s). PY - 2021/1. Y1 - 2021/1. N2 - Melanoma, the most severe form of skin cancer, has poor prognosis and is resistant to chemotherapy. Targeting cancer metabolism is a promising approach in cancer therapeutics. Dihydrolipoyl dehydrogenase (DLD) is a mitochondrial enzyme with diaphorase activity. Here we report a pivotal role of DLD in ...

Saab Automobile recently released the BioPower engines, advertised to use increased turbocharger boost and spark advance on ethanol fuel to enhance performance. Specifications for the 2.0 liter turbocharged engine in the Saab 9-5 Biopower 2.0t report 150 hp (112 kW) on gasoline and a 20% increase to 180 hp (134 kW) on E85 (nominally 85% ethanol, 15% gasoline). While FFVs sold in the U.S. must be emissions certified on Federal Certification Gasoline as well as on E85, the European regulations only require certification on gasoline. Owing to renewed and growing interest in increased ethanol utilization in the U.S., a European-specification 2007 Saab 9-5 Biopower 2.0t was acquired by the Department of Energy and Oak Ridge National Laboratory (ORNL) for benchmark evaluations. Results show that the vehicles gasoline equivalent fuel economy on the Federal Test Procedure (FTP) and the Highway Fuel Economy Test (HFET) are on par with similar U.S.-legal flex-fuel vehicles ...

Saab Automobile recently released the BioPower engines, advertised to use increased turbocharger boost and spark advance on ethanol fuel to enhance performance. Specifications for the 2.0 liter turbocharged engine in the Saab 9-5 Biopower 2.0t report 150 hp (112 kW) on gasoline and a 20% increase to 180 hp (134 kW) on E85 (nominally 85% ethanol, 15% gasoline). While FFVs sold in the U.S. must be emissions certified on Federal Certification Gasoline as well as on E85, the European regulations only require certification on gasoline. Owing to renewed and growing interest in increased ethanol utilization in the U.S., a European-specification 2007 Saab 9-5 Biopower 2.0t was acquired by the Department of Energy and Oak Ridge National Laboratory (ORNL) for benchmark evaluations. Results show that the vehicles gasoline equivalent fuel economy on the Federal Test Procedure (FTP) and the Highway Fuel Economy Test (HFET) are on par with similar U.S.-legal flex-fuel vehicles ...

University of Canterbury Library α-Isopropylmalate synthase (α-IPMS) is responsible for catalysing the first committed step in leucine biosynthesis. This pathway is found in plants and microorganisms, including pathogenic bacteria such as Mycobacterium tuberculosis and Neisseria meningitidis. α-IPMS catalyses a Claisen condensation reaction between α-ketoisovalerate (KIV) and acetyl coenzyme A (AcCoA) to form the product α-isopropylmalate (IPM). This enzyme undergoes feedback inhibition by the end product of the pathway, leucine. This regulation allows the control of the rate leucine biosynthesis. This project focuses on the α-IPMS enzymes from M. tuberculosis and N. meningitidis (MtuIPMS and NmeIPMS). These α-IPMS enzymes are homodimeric in structure. Each monomer consists of a catalytic domain which comprises of a (β/α)8 barrel fold, two subdomains and a regulatory domain, to which the allosteric binding of the natural inhibitor leucine occurs. The mechanism by which the allosteric ...

SUMMARY: The presence of several NADH dehydrogenase activities associated with cytoplasmic membrane vesicles of chemoheterotrophically grown Rhodobacter capsulatus MT1131 was demonstrated by combining isoelectric focusing with NADH-tetranitrobluetetrazolium activity staining, a procedure that should have general applicability in the analysis of bacterial NADH dehydrogenase activities. Low pI (pI = 5.7), Mid pI (pI = 6.9) and High pI (pI = 8.5) bands were resolved. The Mid pI NADH dehydrogenase activity was purified and identified as a dihydrolipoyl dehydrogenase. Our data indicate that this dihydrolipoyl dehydrogenase is derived from a 2-oxoacid dehydrogenase complex which is associated with the cytoplasmic membrane.

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p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.,/p> ,p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.,/p> ,p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).,/p> ,p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x,sup>64,/sup> + x,sup>4,/sup> + x,sup>3,/sup> + x + 1. The algorithm is described in the ISO 3309 standard. ,/p> ,p class=publication>Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.,br /> ,strong>Cyclic redundancy and other checksums,/strong>,br /> ,a href=http://www.nrbook.com/b/bookcpdf.php>Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993),/a>),/p> Checksum:i ...