Characterization of NADP+ binding to perdeuterated MurB: backbone atom NMR assignments and chemical-shift changes

Constantine, Keith L.; Mueller, Luciano; Goldfarb, Valentina; Wittekind, Michael; Metzler, William J.; Yanchunas, Joseph; Robertson, James G.; Malley, Mary F.; Friedrichs, Mark S.; Farmer, Bennett T.

doi:10.1006/jmbi.1997.0915

Cited by 50 publications

(43 citation statements)

References 54 publications

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“…MurB confirmed that both substrates use the same binding pocket of the enzyme; this result is consistent with the role of the bound FAD cofactor in mediating hydride transfer from the NADPH to the UDP-sugar substrate [23]. The maximum number of poses per ligand was set to 30, and no constraints were used to perform molecular docking.…”

Section: Molecular Modeling Studysupporting

confidence: 67%

Design, Synthesis, Antimicrobial Evaluation and Molecular Modeling Study of 1,2,4-Triazole-Based 4-Thiazolidinones

et al. 2016

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A series of 3-(2H-1,2,4-triazol-5-yl)-1,3-thiazolidin-4-one derivatives (7c-l) was designed and synthesized. Their structures have been elucidated based on analytical and spectral data. They were evaluated for their antibacterial and antifungal activities. Compound 7h showed the highest activity against all tested strains, except P. vulgaris, with MIC 8 µg/mL and 4 µg/mL against S. aureus and C. albicans, respectively. Furthermore, Compounds 7c, 7h, and 7j demonstrated moderate anti-mycobacterium activity. The binding mode of the synthesized thiazolidinones to bacterial MurB enzyme was also studied. Good interactions between the docked compounds to the MurB active site were observed primarily with Asn83, Arg310, Arg188 and Ser82 amino acid residues.

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Section: Molecular Modeling Studysupporting

confidence: 67%

Design, Synthesis, Antimicrobial Evaluation and Molecular Modeling Study of 1,2,4-Triazole-Based 4-Thiazolidinones

et al. 2016

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“…The likely docking site of NAD ϩ suggests hydride transfer from the isoalloxazine ring to a pyridine ring positioned at the si face. This unusual stereochemistry was also suggested for the interaction of MurB with NADP ϩ (29).…”

Section: Mmentioning

confidence: 56%

Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S -selanylcysteine

Dobbek

Gremer

Meyer

et al. 1999

Proc. Natl. Acad. Sci. U.S.A.

236

209

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CO dehydrogenase from the aerobic bacterium Oligotropha carboxidovorans catalyzes the oxidation of CO with H 2 O, yielding CO 2 , two electrons, and two H ؉ . Its crystal structure in the air-oxidized form has been determined to 2.2 Å. The active site of the enzyme, which contains molybdenum with three oxygen ligands, molybdopterincytosine dinucleotide and S-selanylcysteine, delivers the electrons to an intramolecular electron transport chain composed of two types of [2Fe-2S] clusters and f lavin-adenine dinucleotide. CO dehydrogenase is composed of an 88.7-kDa molybdoprotein (L), a 30.2-kDa f lavoprotein (M), and a 17.8-kDa iron-sulfur protein (S). It is organized as a dimer of LMS heterotrimers and resembles xanthine dehydrogenase/oxidase in many, but not all, aspects. A mechanism based on a structure with the bound suicide-substrate cyanide is suggested and displays the necessity of S-selanylcysteine for the catalyzed reaction.CO is a trace gas and important scavenger for hydroxyl radicals in the atmosphere. About one fifth of CO [115-230 Tg⅐yr Ϫ1(1)] is used by soil microorganisms (2, 3). CO has a short lifetime within the soil, and consumption of atmospheric CO occurs mainly in the top few centimeters of the humus layer (O horizon), most likely under aerobic conditions. Under aerobic conditions, CO can be used as the sole source of carbon and energy by the carboxidotrophic bacteria, which comprise a taxonomically diverse group of obligate or facultative chemolithoautotrophic species (3, 4). Under anaerobic conditions, CO is used with low affinity by a number of methanogenic archaea and acetogenic, sulfate-reducing, or phototrophic bacteria (3, 5). Generally, anaerobic CO dehydrogenases are nickel-containing [4Fe-4S] proteins. CO dehydrogenases of methanogens or acetogens have acetyl-CoA synthetase activity. CO dehydrogenase (EC 1.2.99.2) of the carboxidotrophic bacterium Oligotropha carboxidovorans is a molybdenum-containing iron-sulfur flavoprotein that catalyzes the oxidation of CO (CO ϩ H 2 O 3 CO 2 ϩ 2e Ϫ ϩ 2H ϩ ) and generates a proton gradient across the cytoplasmic membrane by channeling the electrons formed via cytochrome b 561 into a CO-insensitive respiratory chain (4). O. carboxidovorans uses the reactions of the Calvin cycle for CO 2 fixation (4). In the exponential growth phase, cells of O. carboxidovorans have 87% of CO dehydrogenase associated with the inner aspect of the cytoplasmic membrane and 13% located in the cytoplasm (6).CO dehydrogenase is composed of the 88.7-kDa L (809 residues), 30.2-kDa M (288 residues), and 17.8-kDa S (166 residues) subunits and exists as a dimer of LMS heterotrimers (4). The L subunit carries the molybdenum cofactor, which is a mononuclear complex of Mo and molybdopterin-cytosine dinucleotide (MCD) (7). FAD-binding is on the M subunit and requires conformational changes of M introduced through the binding of M to LS (unpublished data). The S subunit harbors two [2Fe-2S] centers, which are proximal and distal, respectively, to the molybdenum center. They...

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“…5a) Fig. 5b shows the difference between the conformational shifts of the C␣ and C␤ carbons over the entire C-terminal domain, which have been shown to be a convenient method for secondary structure identification in peptides and proteins (35)(36)(37). Overall, the C-terminal domain of Ste20p has helical preferences over most residues (Fig.…”

Section: Conformational Properties Of a 14-residue Gbb Peptide-mentioning

confidence: 98%

Molecular Interactions of the Gβ Binding Domain of the Ste20p/PAK Family of Protein Kinases

Song

Chen

et al. 2001

Journal of Biological Chemistry

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The transmission of the mating signal of the budding yeast Saccharomyces cerevisiae requires Ste20p, a member of the serine/threonine protein kinases of the Ste20p/PAK family, to link the G␤ subunit of the heterotrimeric G protein to the mitogen-activated protein kinase cascades. The binding site of Ste20p to the G␤ subunit was mapped to a consensus sequence of SSLPLI/ VX␤ (X for any residue; for A, I, L, S or T; ␤ for basic residues), which was shown to be a novel G␤ binding ( Biol. Chem. 381, 427-431). Here, we report the results of an NMR study on two GBB motif peptides and the entire C-terminal domain derived from Ste20p. The NMR data show that the two peptide fragments are not uniquely structured in aqueous solution, but in the presence of 40% trifluoroethanol, the longer 37-residue peptide exhibited two well defined, but flexibly linked helical structure elements. Heteronuclear NMR data indicate that the fully functional 86-residue C-terminal domain of Ste20p is again unfolded in aqueous solution but has helical secondary structure preferences similar to those of the two peptide fragments. The NMR results on the two GBB peptides and the entire GBB domain all indicate that the two important binding residues, Ser 879 and Ser 880 , are located at the junction between two helical segments. These experimental observations with the prototype GBB domain of a novel family of G␤-controlled effectors may have important implications in understanding the molecular mechanisms of the signal transduction from the heterotrimeric G protein to the mitogen-activated protein kinase cascade.

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Characterization of NADP+ binding to perdeuterated MurB: backbone atom NMR assignments and chemical-shift changes

Cited by 50 publications

References 54 publications

Design, Synthesis, Antimicrobial Evaluation and Molecular Modeling Study of 1,2,4-Triazole-Based 4-Thiazolidinones

Design, Synthesis, Antimicrobial Evaluation and Molecular Modeling Study of 1,2,4-Triazole-Based 4-Thiazolidinones

Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S -selanylcysteine

Molecular Interactions of the Gβ Binding Domain of the Ste20p/PAK Family of Protein Kinases

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