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Coenzymes (14):
Recent article
Coenzymes
Journal of Virology (84)13 2010
Abstract
We describe the homodimeric crystal structure of PRRSV nsp1beta in its natural, self-processed form. We show that the architecture of its N-terminal domain (NTD) adopts a fold closely resembling that of several known nucleases and has intrinsic nuclease activity that is strongly activated by mangane...
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PMID: 20410261
PDF is available here.
PDF is available here.
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Biochemistry (Washington) (49)18 2010
Abstract
These results reveal species-specific differences in cofactor utilization for PrP(Sc) propagation in vitro and also demonstrate the existence of an endogenous cofactor present in brain tissue not composed of nucleic acids....
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PMID: 20377181
PDF is available here.
PDF is available here.
Abstract
We propose that a different, but also effective, electron-transfer cascade is conserved among the class II photolyases. The existence of such electron transfer pathways is supported by the observation that the catalytically active fully reduced flavin state obtained by photoreduction is maintained e...
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PMID: 20227927
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (114)16 2010
Abstract
We evaluated energetics along the same reaction pathway in aqueous solution modeled by the polarized dielectric and in the virtual enzyme site that included full steric component from the enzyme residues described by molecular mechanics but lacked the electrostatic contribution of these residues. In...
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PMID: 20361776
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (114)16 2010
Abstract
We recently developed a model of mPGES-1 trimer structure by using available crystal structures of both microsomal glutathione transferase-1 (MGST1) and ba3-cytochrome c oxidase as templates. The mPGES-1 trimer model has been used in the present study to examine the detailed binding of mPGES-1 trime...
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PMID: 20369883
PDF is available here.
PDF is available here.
Biotechnology Letters (32)5 2010
Abstract
3,4-Dihydroxybenzoate decarboxylase in Enterobacter cloacae P241 was induced by adding 3,4-dihydroxybenzoic acid, 3-hydroxybenzoic acid, 3,4,5-trihydroxybenzoic acid or 4-acetamidobenzoic acid to the culture medium. After stabilizing the enzyme activity by adding 5 mM dithiothreitol and 20 mM Na(2)S...
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PMID: 20131080
PDF is available here.
PDF is available here.
Pediatrics (125)5 2010
Abstract
We report here the case of a patient who was diagnosed with MoCD at the age of 6 days. Substitution therapy with purified cyclic pyranopterin monophosphate (cPMP) was started on day 36 by daily intravenous administration of 80 to 160 microg of cPMP/kg of body weight. Within 1 to 2 weeks, all urinary...
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PMID: 20385644
PDF is available here.
PDF is available here.
Journal of Biochemistry (147)4 2010
Abstract
Esmond E. Snell (1914-2003) was a giant of B-vitamin and enzyme research. His early research in bacterial nutrition had lead to the discovery of vitamins such as lipoic acid and folic acid, and an anti-vitamin avidin. He developed microbiological assay methods for riboflavin and other vitamins and a...
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PMID: 20353954
PDF is available here.
PDF is available here.
Xenobiotica (40)3 2010
Abstract
We have constructed a stable cell line expressing SULT2A1 by transfection into HEK293 cells. The expression system was used to characterize and compare the sulfation kinetics of DHEA and 15 human bile acids by SULT2A1. Formation of DHEA sulfate demonstrated Michaelis-Menten kinetics with apparent K(...
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PMID: 20102295
PDF is available here.
PDF is available here.
Abstract
We have modeled the 3D structure of Escherichia coli GDH. The geometrical parameters of the homology model structure, validated using the Ramachandran plot, revealed 95.8% of residues in the allowed regions and 2.2% of the residues in disallowed regions. From the model, we have identified five diffe...
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PMID: 20215780
PDF is available here.
PDF is available here.
Acta Crystallographica Section F (65)Pt 12 2009
Abstract
The structure of a probable Mo-cofactor biosynthesis protein B from Sulfolobus tokodaii, belonging to space group P6(4)22 with unit-cell parameters a = b = 136.68, c = 210.52 A, was solved by molecular replacement to a resolution of 1.9 A and refined to an R factor and R(free) of 16.8% and 18.5%, re...
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PMID: 20054111
PDF is available here.
PDF is available here.
Abstract
Xylose reductase is involved in the first step of the fungal pentose catabolic pathway. The gene encoding xylose reductase (Texr) was isolated from the thermophilic fungus Talaromyces emersonii, expressed in Escherichia coli and purified to homogeneity. Texr encodes a 320 amino acid protein with a m...
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PMID: 20093741
PDF is available here.
PDF is available here.
Abstract
We determined pseudovitamin B(12) contents and cobalamin-dependent methionine synthase activity in Synechocystis sp. PCC6803 grown under CoSO(4)-sufficient and -limited conditions. Pseudovitamin B(12) and cobalamin-dependent methionine synthase activity (0.8 nmol/min/mg protein) were found in a homo...
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PMID: 20086323
PDF is available here.
PDF is available here.
Abstract
A fibrinolytic enzyme producing bacterium was isolated and identified as Bacillus subtilis A26 on the basis of the 16S rRNA gene sequence. The fibrin zymography analysis reveals the presence of at least three fibrinolytic enzymes. The crude enzyme exhibited maximal activity at 60 degrees C and pH 8....
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PMID: 19898547
PDF is available here.
PDF is available here.
Journal of General Virology (90)Pt 9 2009
Abstract
We demonstrated that the presence of NS4A allows NS3hel to conserve energy in the course of oligonucleotide substrate unwinding. Using NS4A mutants, we also determined that the C-terminal acidic EELPD/E motif of NS4A, which appears to be functionally similar to the acidic EFDEMEE motif of hepatitis...
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PMID: 19474250
PDF is available here.
PDF is available here.
Abstract
We have expressed two recombinant forms of the P. gingivalis PAD in Escherichia coli, a truncated form with a 43-amino acid N-terminal deletion and the full-length form of PAD as predicted from the DNA sequence. Both forms contain a poly-His tag and Xpress epitope at the N-terminus to aid in detecti...
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PMID: 19545534
PDF is available here.
PDF is available here.
Biotechnology Letters (31)7 2009
Abstract
A major problem when xylose is used for ethanol production is the intercellular redox imbalance arising from different coenzyme specificities of xylose reductase (XR) and xylitol dehydrogenase. The residue Lys21 in XR from Pichia stipitis was subjected to site-directed mutagenesis to alter its coenz...
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PMID: 19330484
PDF is available here.
PDF is available here.
Bioresource Technology (100)9 2009
Abstract
Our results indicated that the biocatalyst from adzuki bean could reduce various aromatic ketones at relatively high concentrations (e.g. 100mM), exhibiting excellent stereoselectivity (>98% e.e.). In addition, it was found that NADPH acts as the reducing cofactor, which can be regenerated by the cr...
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PMID: 19153040
PDF is available here.
PDF is available here.
Abstract
Four different beta-galactosidases (previously named BbgI, BbgII, BbgIII and BbgIV) from Bifidobacterium bifidum NCIMB41171 were overexpressed in Escherichia coli, purified to homogeneity and their biochemical properties and substrate preferences comparatively analysed. BbgI was forming a hexameric...
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PMID: 19099301
PDF is available here.
PDF is available here.
Chemico-Biological Interactions (178)1-3 2009
Abstract
FDH (10-formyltetrahydrofolate dehydrogenase, Aldh1L1, EC 1.5.1.6) converts 10-formyltetrahydrofolate (10-formyl-THF) to tetrahydrofolate and CO(2) in a NADP(+)-dependent reaction. It is a tetramer of four identical 902 amino acid residue subunits. The protein subunit is a product of a natural fusio...
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PMID: 18848533
PDF is available here.
PDF is available here.
Chemico-Biological Interactions (178)1-3 2009
Abstract
We present here a kinetic characterization of the oxidation of the artificial substrate 2,3-dihydro-2,5-dihydroxy-4H-benzopyran-4-one in the presence of NADP(+) by trihydroxynaphthalene reductase from the filamentous fungus Curvularia lunata. Although the experimental data were gathered by conventio...
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PMID: 19071099
PDF is available here.
PDF is available here.
Abstract
We report a novel enzyme designated as diketoreductase (DKR) that was able to reduce two carbonyl groups in a diketo ester to corresponding dihydroxy ester with excellent stereoselectivity. The DKR was cloned from Acinetobacter baylyi by reverse genetic method, heterogeneously expressed in Escherich...
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PMID: 19204834
PDF is available here.
PDF is available here.
Biochemical Society transactions (37)Pt 1 2009
Abstract
The RNA exosome is a multisubunit exonuclease involved in numerous RNA maturation and degradation processes. Exosomes are found in eukaryotes and archaea and are related to bacterial polynucleotide phosphorylates. Over the past years structural and biochemical analysis revealed that archaeal exosome...
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PMID: 19143607
PDF is available here.
PDF is available here.
Abstract
Abstract
Protein metal-coordination sites are richly varied and exquisitely attuned to their inorganic partners, yet many metalloproteins still select the wrong metals when presented with mixtures of elements. Cells have evolved elaborate mechanisms to scavenge for sufficient metal atoms to meet their needs...
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PMID: 19079350
PDF is available here.
PDF is available here.
Biochemical Journal (417)1 2009
Abstract
Mycobacterium tuberculosis FprA (flavoprotein reductase A) is an NAD(P)H- and FAD-binding reductase that is structurally/evolutionarily related to adrenodoxin reductase. Structural analysis implicates Arg(199) and Arg(200) in interactions with the NADP(H) 2'-phosphate group. R199A, R200A and R199A/R...
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PMID: 18767989
PDF is available here.
PDF is available here.
Abstract
We demonstrate that thermal stability of the Tch. tepidum LH1-RC is much higher than that of its mesophilic counterparts, and the enhanced thermal stability requires Ca2+ as a cofactor. Removal of the Ca2+ from Tch. tepidum LH1-RC resulted in a complex with the same degree of thermal stability as th...
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PMID: 18977753
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)5 2008
Abstract
The thiamine diphosphate (ThDP) and metal-ion-dependent enzyme 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-carboxylate synthase, or MenD, catalyze the Stetter-like conjugate addition of alpha-ketoglutarate with isochorismate to release 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexadiene-1-...
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PMID: 18983854
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)52 2008
Abstract
We recently demonstrated that Ct RNR employs a heterobinuclear Mn(IV)/Fe(III) cluster for radical initiation. In essence, the Mn(IV) ion of the cluster functionally replaces the Y(*) of the conventional class I RNR. The Ct beta(2) protein also autoactivates by reaction of its reduced (Mn(II)/Fe(II))...
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PMID: 19061340
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)52 2008
Abstract
These results demonstrate the importance of the unique structural characteristics of the shorter loop in P450BM-3 in establishing the unique redox properties of the FMN in this protein but not its general cytochrome reductase activity....
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PMID: 19055322
PDF is available here.
PDF is available here.
Journal of Physical Chemistry A: Molecules, Spectroscopy, Kinetics, Environment and General Theory (112)50 2008
Abstract
We show, both experimentally and by kinetic modeling, that enzymatic single-turnover (pre-steady-state) H-transfer reactions can be significantly complicated by kinetic isotope fractionation. This fractionation results in the formation of more protiated than deuterated product and is a unique proble...
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PMID: 18847184
PDF is available here.
PDF is available here.
EMBO Journal (27)24 2008
Abstract
We identified an ATPase (tRNA-two-thiouridine C, TtuC) required for the 2-thiolation of s(2)T in Thermus thermophilus and examined in vitro s(2)T formation by TtuC and previously identified s(2)T-biosynthetic proteins (TtuA, TtuB, and cysteine desulphurases). The C-terminal glycine of TtuB is first...
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PMID: 19037260
PDF is available here.
PDF is available here.
Metabolic Brain Disease (23)4 2008
Abstract
Thiamine, in its diphosphate form, is a required cofactor for enzymes of glucose metabolism and branched-chain alpha-ketoacid dehydrogenase (BCKDH). Although metabolic impairments in glucose metabolism have been found to occur in selectively vulnerable brain regions of the thiamine-deficient (TD) br...
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PMID: 18773288
PDF is available here.
PDF is available here.
Journal of Molecular Biology (384)1 2008
Abstract
We showed that MutS bound to a 30-bp heteroduplex containing an unpaired T with a binding affinity approximately 400-fold stronger than to a 30-bp homoduplex, a much higher specificity than previously reported. The binding of nucleotide cofactors decreased both MutS specific and nonspecific binding...
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PMID: 18773911
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)48 2008
Abstract
Mycobacterium tuberculosis (Mtb) cytochrome P450 gene CYP121 is shown to be essential for viability of the bacterium in vitro by gene knock-out with complementation. Production of CYP121 protein in Mtb cells is demonstrated. Minimum inhibitory concentration values for azole drugs against Mtb H37Rv we...
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PMID: 18818197
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)48 2008
Abstract
We present new evidence that riboflavin is present as one of four flavins in Na+-NQR. In particular, we present conclusive evidence that the source of the neutral radical is not one of the FMNs and that riboflavin is the center that gives rise to the neutral flavosemiquinone. The riboflavin is a bon...
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PMID: 18832377
PDF is available here.
PDF is available here.
The Journal of Chemical Physics (129)20 2008
Abstract
We have computed the free energy change Deltamicro(red) associated with one-electron reduction of the flavin ring immersed in water by utilizing the quantum mechanical/molecular mechanical method combined with the theory of energy representation (QM/MM-ER method) recently developed. As a novel treat...
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PMID: 19045881
PDF is available here.
PDF is available here.
Abstract
The class Ic ribonucleotide reductase from Chlamydia trachomatis ( Ct) uses a stable Mn(IV)/Fe(III) cofactor to initiate nucleotide reduction by a free-radical mechanism. Extended X-ray absorption fine structure (EXAFS) spectroscopy and density functional theory (DFT) calculations are used to postul...
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PMID: 18937466
PDF is available here.
PDF is available here.
ChemBioChem (9)16 2008
Abstract
ChemBioChem (9)16 2008
Abstract
Journal of Biological Chemistry (283)45 2008
Abstract
We utilized a site-directed mutagenesis strategy to characterize a putative protein S binding region within the APC Gla domain. Three single amino acid substitutions within the APC Gla domain (D35T, D36A, and A39V) were found to mildly impair protein S-dependent anticoagulant activity (<2-fold) but...
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PMID: 18779332
PDF is available here.
PDF is available here.
Abstract
We used the heterologous expression systems of human sulfite oxidase and Rhodobacter sphaeroides dimethylsulfoxide reductase in E. coli to study the incorporation of different metal ions into the molybdopterin site of these enzymes. From the added metal-containing compounds Na(2)MoO(4), Na(2)WO(4),...
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PMID: 18959753
PDF is available here.
PDF is available here.
Abstract
With a view to their use in the kinetic resolution of racemic non-natural amino acids, five variants of the enzyme L-phenylalanine dehydrogenase, the wild-type enzyme from Bacillus sphaericus and four active-site mutants, have been tested with a range of amino acids. In each case, the rates of react...
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PMID: 19082164
PDF is available here.
PDF is available here.
Archives of Microbiology (190)4 2008
Abstract
Exopolysaccharides (EPS) can affect the rheological properties of foods, act as stabilizers or stimulate preferential growth of bifidobacteria in the gut and therefore function as prebiotics. The latter is referred to fructans, which are synthesized from sucrose by fructosyl transferases (FTFs). In...
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PMID: 18607568
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)40 2008
Abstract
We have recently discovered MetAP inhibitors with selectivity toward different metalloforms of Escherichia coli MetAP, and with these unique inhibitors, we characterized their inhibition of MetAP enzyme activity in a cellular environment. We observed that only inhibitors that are selective for the F...
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PMID: 18669631
PDF is available here.
PDF is available here.
Abstract
We report that NrdI is a flavodoxin counterpart to YfaE for the class Ib RNR. It possesses redox properties unprecedented for a flavodoxin (E(ox/sq) = -264 +/- 17 mV and E(sq/hq) = -255 +/- 17 mV) that allow it to mediate a two-electron reduction of the diferric cluster of NrdF via two successive on...
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PMID: 18799738
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)39 2008
Abstract
We describe high resolution crystal structures for the N(2)-guanine methyltransferase RsmC that modifies residue G1207 in 16 S rRNA near the decoding site of the 30 S ribosomal subunit. RsmC is a class I S-adenosyl-L-methionine-dependent methyltransferase composed of two methyltransferase domains. H...
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PMID: 18667428
PDF is available here.
PDF is available here.
Journal of Molecular Biology (381)5 2008
Abstract
We report the crystal structure of UK from Bacillus anthracis (BA1797) in complex with ATP at 2.82 A resolution. It reveals that the cofactor, in addition to binding in the active sites, also interacts with separate binding pockets located near the center of the hexameric structure. The existence of...
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PMID: 18625239
PDF is available here.
PDF is available here.
Biochemistry (Washington) (47)36 2008
Abstract
We show for the first time that h-prune efficiently hydrolyzes short-chain polyphosphates (k cat of 3-40 s (-1)), including inorganic tripoly- and tetrapolyphosphates and nucleoside 5'-tetraphosphates. Long-chain inorganic polyphosphates (>or=25 phosphate residues) are converted more slowly, whereas...
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PMID: 18700747
PDF is available here.
PDF is available here.
Journal of Biological Chemistry (283)37 2008
Abstract
We investigated the involvement of the human L-cysteine desulfurase Nfs1 in sulfur transfer to MOCS3-RLD. A variant of Nfs1 was purified in conjunction with Isd11 in a heterologous expression system in Escherichia coli, and the kinetic parameters of the purified protein were determined. By studying...
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PMID: 18650437
PDF is available here.
PDF is available here.
Abstract
Over the last decade, protein purification has become more efficient and standardized through the introduction of affinity tags. The choice and position of the tag, however, can directly influence the process of protein crystallization. Octopine dehydrogenase (OcDH) without a His tag and tagged prot...
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PMID: 18765918
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1777)9 2008
Abstract
We found that the formation and decay of the S(1)Tyr(Z) EPR signal were independent of the treatment of K(3)Fe(CN)(6), whereas formation and decay of the Car(+)/Chl(Z)(+) EPR signal correlated with the reduction and recovery of the Fe(3+) EPR signal of the non-heme iron in K(3)Fe(CN)(6) pre-treated...
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PMID: 18510941
PDF is available here.
PDF is available here.
Biophysical Journal (95)5 2008
Abstract
We study how a mechanical force opposing the forward motion of the enzyme along DNA affects the translocation rate. We also study the influence of nucleotide and magnesium concentration on this process. The experiment shows that the opposing mechanical force is a competitive inhibitor of nucleotide...
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PMID: 18708471
PDF is available here.
PDF is available here.
Abstract
We show direct biochemical evidence for the role of NifQ in FeMo-co biosynthesis. As-isolated NifQ was found to carry a molybdenum-iron-sulfur cluster that serves as a specific molybdenum donor for FeMo-co biosynthesis. Purified NifQ supported in vitro FeMo-co synthesis in the absence of an addition...
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PMID: 18697927
PDF is available here.
PDF is available here.
Abstract
Abstract
The oligomeric state and the hydrodynamic properties of human respiratory syncytial virus (HRSV) phosphoprotein (P), a known cofactor of the viral RNA-dependent RNA polymerase (L), and a trypsin-resistant fragment (X) that includes its oligomerization domain were analyzed by sedimentation equilibriu...
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PMID: 18300250
PDF is available here.
PDF is available here.
Abstract
Infrared data for mono-iron complexes possessing two cis-CO together with Mössbauer data for the enzyme and a model complex support the assignment that the iron centre of the cluster-free hydrogenase Hmd is low-spin Fe(II).
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PMID: 18654711
PDF is available here.
PDF is available here.
Abstract
The crystal structure of human 20alpha-hydroxysteroid dehydrogenase (AKR1C1) in ternary complex with the coenzyme NADP (+) and the potent inhibitor 3,5-dichlorosalicylic acid was determined at a resolution of 1.8 A. The inhibitor is held in place by a network of hydrogen bonding interactions with th...
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PMID: 18620380
PDF is available here.
PDF is available here.
Abstract
We describe evidence that pMMO is a multicopper protein. Its unique trinuclear copper cluster mediates dioxygen chemistry and O-atom transfer during alkane hydroxylation. Although a recent crystal structure did not show this tricopper cluster, we provide compelling evidence for such a cluster throug...
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PMID: 18605740
PDF is available here.
PDF is available here.
Abstract
We proposed a modified Chou's pseudo-amino acid composition method to extract features from sequences and the k-nearest neighbor was used as the classifier, and the results were very encouraging. When lambda = 48, w = 0.1, the areas under the ROC curve of k-nearest neighbor in 10-fold cross-validati...
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PMID: 18998548
PDF is available here.
PDF is available here.