Search

Your search keyword '"Herzberg, O"' showing total 276 results
Start Over Author "Herzberg, O"
276 results on '"Herzberg, O"'

2. BB0238 from Borrelia burgdorferi

Author

Brangulis, K., primary, Foor, S.D., additional, Shakya, A.K., additional, Rana, V.S., additional, Bista, S., additional, Kitsou, C., additional, Ronzetti, M., additional, Linden, S.B., additional, Altieri, A.S., additional, Akopjana, I., additional, Baljinnyam, B., additional, Nelson, D.C., additional, Simeonov, A., additional, Herzberg, O., additional, Caimano, M.J., additional, and Pal, U., additional

Published
2023
Full Text
View/download PDF

3. BB0238 from Borrelia burgdorferi, Se-Met data for Leu240Met mutant

Author

Brangulis, K., primary, Foor, S.D., additional, Shakya, A.K., additional, Rana, V.S., additional, Bista, S., additional, Kitsou, C., additional, Ronzetti, M., additional, Linden, S.B., additional, Altieri, A.S., additional, Akopjana, I., additional, Baljinnyam, B., additional, Nelson, D.C., additional, Simeonov, A., additional, Herzberg, O., additional, Caimano, M.J., additional, and Pal, U., additional

Published
2023
Full Text
View/download PDF

8. Degradation pathway of the phosphonate ciliatine: crystal structure of 2-aminoethylphosphonate transaminase

Author

Chen, Celia C. H., Zhang, H., Kim, A. D., Howard, A., Sheldrick, G. M., Mariano-Dunaway, D., and Herzberg, O.

Subjects
Biochemistry -- Research, Amines, Diffraction -- Research, Biological sciences, Chemistry
Abstract

Research has been conducted on 2-aminoethylphosphonate transaminase. The study of the crystal structure of this 2-aminoethylphosphonate transaminase carried out via multiwavelength anomalous diffraction of selenium atoms is presented.

Published
2002

14. Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016)

Author

Kryshtafovych, A, Albrecht, R, Baslé, A, Bule, P, Caputo, A, Carvalho, A, Chao, K, Diskin, R, Fidelis, K, Fontes, C, Fredslund, F, Gilbert, H, Goulding, C, Hartmann, M, Hayes, C, Herzberg, O, Hill, J, Joachimiak, A, Kohring, G, Koning, R, Lo Leggio, L, Mangiagalli, M, Michalska, K, Moult, J, Najmudin, S, Nardini, M, Nardone, V, Ndeh, D, Nguyen, T, Pintacuda, G, Postel, S, Van Raaij, M, Roversi, P, Shimon, A, Singh, A, Sundberg, E, Tars, K, Zitzmann, N, Schwede, T, Kryshtafovych, A, Albrecht, R, Baslé, A, Bule, P, Caputo, A, Carvalho, A, Chao, K, Diskin, R, Fidelis, K, Fontes, C, Fredslund, F, Gilbert, H, Goulding, C, Hartmann, M, Hayes, C, Herzberg, O, Hill, J, Joachimiak, A, Kohring, G, Koning, R, Lo Leggio, L, Mangiagalli, M, Michalska, K, Moult, J, Najmudin, S, Nardini, M, Nardone, V, Ndeh, D, Nguyen, T, Pintacuda, G, Postel, S, Van Raaij, M, Roversi, P, Shimon, A, Singh, A, Sundberg, E, Tars, K, Zitzmann, N, and Schwede, T

Abstract

The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment

Published
2018

15. Probing the calcium-induce conformational transition of troponin C with site-directed mutants

Author

Fujimori, K., Sorenson, M., Herzberg, O., Moult, J., and Reinach, F.C.

Subjects
Muscle contraction -- Research, Muscle proteins -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Contraction of cardiac and skeletal muscle is regulated by binding calcium to troponin, which contains three subunits with distinct activities: troponin C, troponin I, and troponin T. The troponin C molecule has been isolated, purified and examined by X-ray crystallography so that its three-dimensional structure is known. The calcium molecule induces changes in the shape of the troponin C molecule. Using site-directed mutagenesis (in which a particular area of the DNA that encodes the gene is altered), the sites and the mechanism of muscle contraction regulation can be studied. The regulatory sites have been identified to be sites which bind calcium at one end of the troponin molecule. The molecule was bridged together using site-directed mutagenesis, which inhibited the mobility of the molecule and the binding of calcium. The altered troponin molecule was introduced into muscle fibers and muscle contraction was no longer regulated, indicating that these changes affected other molecules involved in muscle contraction. These studies will lead to the further understanding of how muscle contraction occurs and how it is regulated. (Consumer Summary produced by Reliance Medical Information, Inc.)

Published
1990

20. Standard numbering scheme for class B beta-lactamases

Author

Galleni, M, Lamotte Brasseur, J., Rossolini, G. M., Spencer, J., Dideberg, O., Frère, J. M., Amicosante, Gianfranco, Franceschini, Nicola, Bush, K., Concha, N. O., Herzberg, O., Livermore, D. M., Rasmussen, B. A., Rodrigues, J., Saavedra, M. J., Sutton, B., Fabiane, S. M., and Toney, J. H.

Subjects
Pharmacology, Scheme (programming language), Sequence, Bacteria, Sequence Homology, Amino Acid, Protein Conformation, β lactamases, Molecular Sequence Data, Computational biology, Biology, beta-Lactamases, Numbering, Conserved sequence, Infectious Diseases, Protein structure, Numbering scheme, Biochemistry, Guest Commentary, Pharmacology (medical), Amino Acid Sequence, Peptide sequence, computer, Conserved Sequence, computer.programming_language
Abstract

Unlike for classes A and B, a standardized amino acid numbering scheme has not been proposed for the class C (AmpC) β-lactamases, which complicates communication in the field. Here, we propose a scheme developed through a collaborative approach that considers both sequence and structure, preserves traditional numbering of catalytically important residues (Ser64, Lys67, Tyr150, and Lys315), is adaptable to new variants or enzymes yet to be discovered and includes a variation for genetic and epidemiological applications.

Published
2001

21. Structure and function of 2,3-dimethylmalate lyase, a PEP mutase/isocitrate lyase superfamily member.

Author

Narayanan, B., Niu, W., Joosten, H.J., Li, Z., Kuipers, R.K.P., Schaap, P.J., Dunaway-Mariano, D., Herzberg, O., Narayanan, B., Niu, W., Joosten, H.J., Li, Z., Kuipers, R.K.P., Schaap, P.J., Dunaway-Mariano, D., and Herzberg, O.

Abstract

Contains fulltext : 81453.pdf (publisher's version ) (Closed access), The Aspergillus niger genome contains four genes that encode proteins exhibiting greater than 30% amino acid sequence identity to the confirmed oxaloacetate acetyl hydrolase (OAH), an enzyme that belongs to the phosphoenolpyruvate mutase/isocitrate lyase superfamily. Previous studies have shown that a mutant A. niger strain lacking the OAH gene does not produce oxalate. To identify the function of the protein sharing the highest amino acid sequence identity with the OAH (An07g08390, Swiss-Prot entry Q2L887, 57% identity), we produced the protein in Escherichia coli and purified it for structural and functional studies. A focused substrate screen was used to determine the catalytic function of An07g08390 as (2R,3S)-dimethylmalate lyase (DMML): k(cat)=19.2 s(-1) and K(m)=220 microM. DMML also possesses significant OAH activity (k(cat)=0.5 s(-1) and K(m) =220 microM). DNA array analysis showed that unlike the A. niger oah gene, the DMML encoding gene is subject to catabolite repression. DMML is a key enzyme in bacterial nicotinate catabolism, catalyzing the last of nine enzymatic steps. This pathway does not have a known fungal counterpart. BLAST analysis of the A. niger genome for the presence of a similar pathway revealed the presence of homologs to only some of the pathway enzymes. This and the finding that A. niger does not thrive on nicotinamide as a sole carbon source suggest that the fungal DMML functions in a presently unknown metabolic pathway. The crystal structure of A. niger DMML (in complex with Mg(2+) and in complex with Mg(2+) and a substrate analog: the gem-diol of 3,3-difluoro-oxaloacetate) was determined for the purpose of identifying structural determinants of substrate recognition and catalysis. Structure-guided site-directed mutants were prepared and evaluated to test the contributions made by key active-site residues. In this article, we report the results in the broader context of the lyase branch of the phosphoenolpyruvate mutase/isocitrate lyas

Published
2009

22. Structural consequences of the active site substitution Cys181 ==> Ser in metallo-beta-lactamase from Bacteroides fragilis

Author

Li, Z., Rasmussen, B. A., and Herzberg, O.

Subjects
Bacteroides fragilis, Models, Molecular, Zinc, Binding Sites, Amino Acid Substitution, Protein Conformation, Serine, Cysteine, beta-Lactamases, Research Article
Abstract

The metallo-beta-lactamases require divalent cations such as zinc or cadmium for hydrolyzing the amide bond of beta-lactam antibiotics. The crystal structure of the Zn2+ -bound enzyme from Bacteroides fragilis contains a binuclear zinc center in the active site. A hydroxide, coordinated to both zinc atoms, is proposed as the moiety that mounts the nucleophilic attack on the carbonyl carbon atom of the beta-lactam bond of the substrate. It was previously reported that the replacement of the active site Cys181 by a serine residue severely impaired catalysis while atomic absorption measurements indicated that binding of the two zinc ions remained intact. Contradicting data emerge from recent mass spectrometry results, which show that only a single zinc ion binds to the C181S metallo-beta-lactamase. In the current study, the C181S mutant enzyme was examined at the atomic level by determining the crystal structure at 2.6 A resolution. The overall structure of the mutant enzyme is the same as that of the wild-type enzyme. At the mutation site, the side chain of Ser181 occupies the same position as that of the side chain of Cys181 in the wild-type protein. One zinc ion, Zn1, is present in the crystal structure; however, the site of the second zinc ion, Zn2 is unoccupied. A water molecule is associated with Zn1, reminiscent of the hydroxide seen in the structure of the wild-type enzyme but farther from the metal. The position of the water molecule is off the plane of the carboxylate group of Asp103; therefore, the water molecule may be less nucleophilic than a water molecule which is coplanar with the carboxylate group.

Published
1999

Catalog

Books, media, physical & digital resources
See catalog results