scholarly journals Probing the determinants of protein stability: comparison of class A β-lactamases

1995 ◽  
Vol 308 (3) ◽  
pp. 859-864 ◽  
Author(s):  
M Vanhove ◽  
S Houba ◽  
J Lamotte-Brasseur ◽  
J M Frère
Keyword(s):  
Amino Acid ◽  
Hydrogen Bonds ◽  
Bacterial Species ◽  
Three Dimensional ◽  
Peptide Bond ◽  
Minor Role ◽  
Salt Bridges ◽  
Beta Lactamases ◽  
Class A ◽  
Intramolecular Hydrogen

Five class A beta-lactamases produced by various mesophilic bacterial species have been compared. Although closely related in primary and overall structures, these enzymes exhibit very different stabilities. In order to investigate the factors responsible for these differences, several features deduced from the amino acid composition and three-dimensional structures were studied for the five proteins. This analysis revealed that higher stability appeared to correlate with increased numbers of intramolecular hydrogen bonds and of salt bridges. By contrast, the global hydrophobicity of the protein seemed to play a relatively minor role. A strongly unfavourable balance between charged residues and the presence of a cis-peptide bond preceding a non-proline residue might also contribute to the particularly low stability of two of the enzymes.

scholarly journals Bis(lysine-κ2 N,O)hexa-μ2-oxido-hexaoxidobis(1,10-phenanthroline-κ2 N,N′)dicopper(II)tetravanadium(V) tetrahydrate

IUCrData ◽  
2017 ◽  
Vol 2 (7) ◽  
Author(s):  
Ana Karen Giron-Moreno ◽  
Nancy Lara-Sánchez ◽  
Gabriela Moreno-Martínez ◽  
Cándida Pastor-Ramírez ◽  
Eduardo Sánchez-Lara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Water Molecules ◽  
Formula Unit ◽  
Zwitterionic Form ◽  
Solvent Water ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The heterometallic coordination compound [Cu(Lys)(phen)]2V4O12·4H2O (Lys is the amino acid lysine, C6H14N2O2, and phen is 1,10-phenanthroline, C12H8N2) lies across an inversion centre. Two [Cu(Lys)(phen)]2+ units coordinate to the cyclo-vanadate fragment and the formula unit is completed by four solvent water molecules. The lysine ligand is in the zwitterionic form and chelates the CuII atom via the α-NH2 and α-COO− donor groups, while the ∊-NH3 + group is involved in intramolecular hydrogen bonds with the central [V4O12]4− core and with solvent water molecules. In the crystal, N—H...O and O—H...O hydrogen bonds connect the components of the structure to form a three-dimensional network. The crystal structure is further stabilized by π–π interactions involving the phen ligands. The lysine group is disordered over two sets of sites with refined occupancies of 0.534 (11) and 0.466 (11).

scholarly journals Amino acid sequence of the penicillin-binding protein/dd-peptidase of Streptomyces K15. Predicted secondary structures of the low Mr penicillin-binding proteins of class A

1991 ◽  
Vol 279 (1) ◽  
pp. 223-230 ◽  
Author(s):  
P Palomeque-Messia ◽  
S Englebert ◽  
M Leyh-Bouille ◽  
M Nguyen-Distèche ◽  
C Duez ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Active Sites ◽  
Binding Protein ◽  
Secondary Structures ◽  
Peptide Sequence ◽  
Penicillin Binding Protein ◽  
Signal Peptide Sequence ◽  
Beta Lactamases ◽  
Class A

The low-Mr penicillin-binding protein (PBP)/DD-transpeptidase of Streptomyces K15 is synthesized in the form of a 291-amino acid-residue precursor possessing a cleavable 29-amino acid-residue signal peptide. Sequence-similarity searches and hydrophobic-cluster analysis show that the Streptomyces K15 enzyme, the Escherichia coli PBPs/DD-carboxy-peptidases 5 and 6, the Bacillus subtilis PBP/DD-carboxypeptidase 5 and the spoIIA product (a putative PBP involved in the sporulation of B. subtilis) are structurally related and form a distinct class A of low-Mr PBPs/DD-peptidases. The distribution of the hydrophobic clusters along the amino acid sequences also shows that the Streptomyces K15 PBP, and by extension the other PBPs of class A, have similarity in the polypeptide folding, with the beta-lactamases of class A, with as reference the Streptomyces albus G and Staphylococcus aureus beta-lactamases of known three-dimensional structure. This comparison allows one to predict most of the secondary structures in the PBPs and the amino acid motifs that define the enzyme active sites.

scholarly journals Characterization of beta-lactamase gene blaPER-2, which encodes an extended-spectrum class A beta-lactamase.

1996 ◽  
Vol 40 (3) ◽  
pp. 616-620 ◽  
Author(s):  
A Bauernfeind ◽  
I Stemplinger ◽  
R Jungwirth ◽  
P Mangold ◽  
S Amann ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Beta Lactamase ◽  
Reading Frame ◽  
Beta Lactamases ◽  
Class A ◽  
Extended Spectrum ◽  
The Family ◽  
Extended Spectrum Beta Lactamases ◽  
Lactamase Gene

Plasmidic extended-spectrum beta-lactamases of Ambler class A are mostly inactive against ceftibuten. Salmonella typhimurium JMC isolated in Argentina harbors a bla gene located on a plasmid (pMVP-5) which confers transferable resistance to oxyiminocephalosporins, aztreonam, and ceftibuten. The beta-lactamase PER-2 (formerly ceftibutenase-1; CTI-1) is highly susceptible to inhibition by clavulanate and is located at a pI of 5.4 after isoelectric focusing. The blaPER-2 gene was cloned and sequenced. The nucleotide sequence of a 2.2-kb insert in vector pBluescript includes an open reading frame of 927 bp. Comparison of the deduced amino acid sequence of PER-2 with those of other beta-lactamases indicates that PER-2 is not closely related to TEM or SHV enzymes (25 to 26% homology). PER-2 is most closely related to PER-1 (86.4% homology), an Ambler class A enzyme first detected in Pseudomonas aeruginosa. An enzyme with an amino acid sequence identical to that of PER-1, meanwhile, was found in various members of the family Enterobacteriaceae isolated from patients in Turkey. Our data indicate that PER-2 and PER-1 represent a new group of Ambler class A extended-spectrum beta-lactamases. PER-2 so far has been detected only in pathogens (S. typhimurium, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis) isolated from patients in South America, while the incidence of PER-1-producing strains so far has been restricted to Turkey, where it occurs both in members of the family Enterobacteriaceae and in P. aeruginosa.

PREDICTION OF THE THREE-DIMENSIONAL STRUCTURE OF THE ENZYMATIC PART OF T-PA

1987 ◽  
Author(s):  
A Heckel ◽  
K M Hasselbach
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Active Site ◽  
Serine Proteases ◽  
Three Dimensional ◽  
Amino Acid Sequences ◽  
Dimensional Structure ◽  
Salt Bridges ◽  
Three Dimensional Structure ◽  
Insertions And Deletions

Up to now the three-dimensional structure of t-PA or parts of this enzyme is unknown. Using computer graphical methods the spatial structure of the enzymatic part of t-PA is predicted on the hypothesis, the three-dimensional backbone structure of t-PA being similar to that of other serine proteases. The t-PA model was built up in three steps:1) Alignment of the t-PA sequence with other serine proteases. Comparison of enzyme structures available from Brookhaven Protein Data Bank proved elastase as a basis for modeling.2) Exchange of amino acids of elastase differing from the t-PA sequence. The replacement of amino acids was performed such that backbone atoms overlapp completely and side chains superpose as far as possible.3) Modeling of insertions and deletions. To determine the spatial arrangement of insertions and deletions parts of related enzymes such as chymotrypsin or trypsin were used whenever possible. Otherwise additional amino acid sequences were folded to a B-turn at the surface of the proteine, where all insertions or deletions are located. Finally the side chain torsion angles of amino acids were optimised to prevent close contacts of neigh bouring atoms and to improve hydrogen bonds and salt bridges.The resulting model was used to explain binding of arginine 560 of plasminogen to the active site of t-PA. Arginine 560 interacts with Asp 189, Gly 19 3, Ser 19 5 and Ser 214 of t-PA (chymotrypsin numbering). Furthermore interaction of chromo-genic substrate S 2288 with the active site of t-PA was studied. The need for D-configuration of the hydrophobic amino acid at the N-terminus of this tripeptide derivative could be easily explained.

scholarly journals N-(β-Carboxyethyl)-α-isoleucine

2013 ◽  
Vol 69 (2) ◽  
pp. o172-o173 ◽  
Author(s):  
Irene Nehls ◽  
Olaf Hanebeck ◽  
Roland Becker ◽  
Franziska Emmerling
Keyword(s):  
Crystal Structure ◽  
Biological Activity ◽  
Amino Acid ◽  
Hydrogen Bonds ◽  
Title Compound ◽  
Addition Reaction ◽  
Three Dimensional ◽  
Dimensional Network

The title compound, {2-[(2-carbamoylethyl)amino]-3-methylpentanoic acid}, C9H18N2O3, is of interest with respect to its biological activity. It was formed during an addition reaction between acrylamide and the amino acid isoleucine. The crystal structure is a three-dimensional network built up by intermolecular N—H...O and O—H...N hydrogen bonds.

N.M.R. studies of myelin basic protein. XII. Spectra in aqueous solution of a synthetic octapeptide encephalitogenic in the Lewis rat

1984 ◽  
Vol 37 (7) ◽  
pp. 1427 ◽  
Author(s):  
J Bremer ◽  
WJ Moore
Keyword(s):  
Aqueous Solution ◽  
Hydrogen Bonds ◽  
Synthetic Peptide ◽  
Basic Protein ◽  
Peptide Bond ◽  
Lewis Rat ◽  
Compact Structure ◽  
Linear Peptide ◽  
Temperature Dependences ◽  
Intramolecular Hydrogen

A synthetic peptide Ala-Gln-Arg-Pro-Gln-Asp-Glu-Asn encephalitogenic in the Lewis rat has been studied in aqueous solutions by 1H and 13C n.m.r. The configuration about the Arg-Pro peptide bond is > 99% trans. The temperature dependences and titration shifts of NH resonances areconsistent with occurrence of a number of intramolecular hydrogen bonds, leading to an unusually compact structure for a linear peptide in aqueous solution.

scholarly journals Sequences of beta-lactamase genes encoding CTX-M-1 (MEN-1) and CTX-M-2 and relationship of their amino acid sequences with those of other beta-lactamases.

1996 ◽  
Vol 40 (2) ◽  
pp. 509-513 ◽  
Author(s):  
A Bauernfeind ◽  
I Stemplinger ◽  
R Jungwirth ◽  
S Ernst ◽  
J M Casellas
Keyword(s):  
Amino Acid ◽  
Klebsiella Oxytoca ◽  
Amino Acid Sequences ◽  
Protein Sequencing ◽  
Beta Lactamase ◽  
Beta Lactamases ◽  
Class A ◽  
Men 1 ◽  
Genes Encoding ◽  
Relationship Of

Amino acid sequences determined either by protein sequencing or by DNA sequencing are identical for cefotaximases CTX-M-1 and MEN-1, whereas CTX-M-2 is 84% identical to CTX-M-1/MEN-1. Both beta-lactamases are distantly related to other plasmidic class A enzymes (homology to TEM-1 is 38.1% for CTX-M-1/MEN-1 and 36.5% for CTX-M-2); the closest relationship was with the chromosomal beta-lactamase of Klebsiella oxytoca E23004 (homologies of 74.5% for CTX-M-1/MEN-1 and 77.9% for CTX-M-2). The cefotaximases CTX-M-1/MEN-1 and CTX-M-2 represent two members of a new subgroup of plasmidic class A beta-lactamases.

Two polymorphs ofN-(2-methoxyphenyl)-4-oxo-4H-chromone-3-carboxamide

2013 ◽  
Vol 69 (8) ◽  
pp. 927-933 ◽  
Author(s):  
Ligia R. Gomes ◽  
John Nicolson Low ◽  
Fernanda Borges ◽  
Fernando Cagide
Keyword(s):  
Hydrogen Bonds ◽  
Molecular Conformation ◽  
Three Dimensional ◽  
Amide Group ◽  
Monoclinic Space Group ◽  
Asymmetric Unit ◽  
Intramolecular Hydrogen Bonds ◽  
Compound C ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The title compound, C17H13NO4, crystallizes in two polymorphic forms, each with two molecules in the asymmetric unit and in the monoclinic space groupP21/c. All of the molecules have intramolecular hydrogen bonds involving the amide group. The amide N atoms act as donors to the carbonyl group of the pyrone and also to the methoxy group of the benzene ring. The carbonyl O atom of the amide group acts as an acceptor of the β and β′ C atoms belonging to the aromatic rings. These intramolecular hydrogen bonds have a profound effect on the molecular conformation. In one polymorph, the molecules in the asymmetric unit are linked to form dimers by weak C—H...O interactions. In the other, the molecules in the asymmetric unit are linked by a single weak C—H...O hydrogen bond. Two of these units are linked to form centrosymmetric tetramers by a second weak C—H...O interaction. Further interactions of this type link the molecules into chains, so forming a three-dimensional network. These interactions in both polymorphs are supplemented by π–π interactions between the chromone rings and between the chromone and methoxyphenyl rings.

scholarly journals Carboxy groups as essential residues in β-lactamases

1986 ◽  
Vol 240 (1) ◽  
pp. 215-219 ◽  
Author(s):  
C Little ◽  
E L Emanuel ◽  
J Gagnon ◽  
S G Waley
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Bacillus Cereus ◽  
Bacillus Licheniformis ◽  
Enterobacter Cloacae ◽  
Amino Acid Sequences ◽  
Beta Lactamase ◽  
Beta Lactamases ◽  
Class A

Beta-lactamases are divided into classes A, B and C on the basis of their amino acid sequences. Beta-Lactamases were incubated at pH 4.0 with the carboxy-group reagent 1-(3-dimethylaminopropyl)-3-ethylcarbodi-imide plus a coloured nucleophile and the extents of inactivation and nucleophile incorporation were monitored. Two class A enzymes (from Bacillus cereus and Bacillus licheniformis) and two class C enzymes (from Enterobacter cloacae P99 and Pseudomonas aeruginosa) were examined. All four enzymes were inactivated, with total inactivation corresponding to the incorporation of approx. 2-3 mol of nucleophile/mol of enzyme. In the case of beta-lactamase I from Bacillus cereus, some 53% of the incorporated nucleophile was located on glutamic acid-168 in the amino acid sequence.

2,3-Dihydro-7,8-dihydroxy-3-[(4-methoxyphenyl)methylene]-4H-1-benzopyran-4-one

2006 ◽  
Vol 62 (4) ◽  
pp. o1254-o1256 ◽  
Author(s):  
Suchada Chantrapromma ◽  
Sompong Boonsri ◽  
Hoong-Kun Fun ◽  
Shazia Anjum ◽  
Akkharawit Kanjana-opas
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interactions ◽  
Title Compound ◽  
Three Dimensional ◽  
Molecular Network ◽  
Pyran Ring ◽  
Intramolecular Hydrogen Bonds ◽  
One Dimensional ◽  
Intramolecular Hydrogen ◽  
First Time

The title compound, also known as intricatinol, C17H14O5, is a homoisoflavanoid that was isolated for the first time from the twigs and stems of Caesalpinia digyna Rottler. The pyran ring is in an envelope form. O—H...O intramolecular hydrogen bonds are observed. Symmetry-related molecules are linked via O—H...O intermolecular interactions to form infinite one-dimensional chains. These chains are interconnected to form a three-dimensional molecular network.

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