scholarly journals Identification of the potential active site of the septal peptidoglycan polymerase FtsW

PLoS Genetics ◽  
2022 ◽  
Vol 18 (1) ◽  
pp. e1009993
Author(s):  
Ying Li ◽  
Adrien Boes ◽  
Yuanyuan Cui ◽  
Shan Zhao ◽  
Qingzhen Liao ◽  
...  
Keyword(s):  
Active Site ◽  
Dominant Negative ◽  
Central Cavity ◽  
Penicillin Binding Proteins ◽  
Division Site ◽  
Lipid Ii ◽  
Extracellular Loops ◽  
Class B ◽  
New Antibiotics ◽  
Dominant Negative Mutations

SEDS (Shape, Elongation, Division and Sporulation) proteins are widely conserved peptidoglycan (PG) glycosyltransferases that form complexes with class B penicillin-binding proteins (bPBPs, with transpeptidase activity) to synthesize PG during bacterial cell growth and division. Because of their crucial roles in bacterial morphogenesis, SEDS proteins are one of the most promising targets for the development of new antibiotics. However, how SEDS proteins recognize their substrate lipid II, the building block of the PG layer, and polymerize it into glycan strands is still not clear. In this study, we isolated and characterized dominant-negative alleles of FtsW, a SEDS protein critical for septal PG synthesis during bacterial cytokinesis. Interestingly, most of the dominant-negative FtsW mutations reside in extracellular loops that are highly conserved in the SEDS family. Moreover, these mutations are scattered around a central cavity in a modeled FtsW structure, which has been proposed to be the active site of SEDS proteins. Consistent with this, we found that these mutations blocked septal PG synthesis but did not affect FtsW localization to the division site, interaction with its partners nor its substrate lipid II. Taken together, these results suggest that the residues corresponding to the dominant-negative mutations likely constitute the active site of FtsW, which may aid in the design of FtsW inhibitors.

Dominant-negative mutations in PPAR alpha are present in unselected human populations and have a metabolic signature

2018 ◽  
Author(s):  
Audrey Melvin ◽  
Brian Lam ◽  
Claudia Langenberg ◽  
Maura Agostini ◽  
Erik Schoenmakers ◽  
...  
Keyword(s):  
Dominant Negative ◽  
Human Populations ◽  
Ppar Alpha ◽  
Metabolic Signature ◽  
Dominant Negative Mutations

scholarly journals Systematic Analysis of Metallo-β-Lactamases Using an Automated Database

2012 ◽  
Vol 56 (7) ◽  
pp. 3481-3491 ◽  
Author(s):  
Michael Widmann ◽  
Jürgen Pleiss ◽  
Peter Oelschlaeger
Keyword(s):  
Active Site ◽  
Hot Spots ◽  
Bacterial Resistance ◽  
Protein Sequences ◽  
Database System ◽  
Systematic Analysis ◽  
Link Type ◽  
Peptide Database ◽  
Class B ◽  
Automated Database

ABSTRACTMetallo-β-lactamases (MBLs) are enzymes that hydrolyze β-lactam antibiotics, resulting in bacterial resistance to these drugs. These proteins have caused concerns due to their facile transference, broad substrate spectra, and the absence of clinically useful inhibitors. To facilitate the classification, nomenclature, and analysis of MBLs, an automated database system was developed, the Metallo-β-Lactamase Engineering Database (MBLED) (http://www.mbled.uni-stuttgart.de). It contains information on MBLs retrieved from the NCBI peptide database while strictly following the nomenclature by Jacoby and Bush (http://www.lahey.org/Studies/) and the generally accepted class B β-lactamase (BBL) standard numbering scheme for MBLs. The database comprises 597 MBL protein sequences and enables systematic analyses of these sequences. A systematic analysis employing the database resulted in the generation of mutation profiles of assigned IMP- and VIM-type MBLs, the identification of five MBL protein entries from the NCBI peptide database that were inconsistent with the Jacoby and Bush nomenclature, and the identification of 15 new IMP candidates and 9 new VIM candidates. Furthermore, the database was used to identify residues with high mutation frequencies and variability (mutation hot spots) that were unexpectedly distant from the active site located in the ββ sandwich: positions 208 and 266 in the IMP family and positions 215 and 258 in the VIM family. We expect that the MBLED will be a valuable tool for systematically cataloguing and analyzing the increasing number of MBLs being reported.

1.85 Å Resolution Structure of the ZincII β-Lactamase from Bacillus cereus

1998 ◽  
Vol 54 (3) ◽  
pp. 313-323 ◽  
Author(s):  
Andrea Carfi ◽  
Emile Duée ◽  
Moreno Galleni ◽  
Jean-Marie Frère ◽  
Otto Dideberg
Keyword(s):  
Bacillus Cereus ◽  
Active Site ◽  
Metal Ion ◽  
Wide Spectrum ◽  
Zinc Ion ◽  
Beta Lactamases ◽  
Carbonate Ion ◽  
Class B ◽  
Bivalent Metal Ions ◽  
Using Data

Class B \beta-lactamases are wide spectrum enzymes which require bivalent metal ions for activity. The structure of the class B zinc-ion-dependent β-lactamase from Bacillus cereus (BCII) has been refined at 1.85 Å resolution using data collected on cryocooled crystals (100 K). The enzyme from B. cereus has a molecular mass of 24 946 Da and is folded into a \beta-sandwich structure with helices on the external faces. The active site is located in a groove running between the two \beta-sheets [Carfi et al. (1995). EMBO J. 14, 4914–4921]. The 100 K high-resolution BCII structure shows one fully and one partially occupied zinc site. The zinc ion in the fully occupied site (the catalytic zinc) is coordinated by three histidines and one water molecule. The second zinc ion is at 3.7 Å from the first one and is coordinated by one histidine, one cysteine, one aspartate and one unknown molecule (which is most likely to be a carbonate ion). In the B. cereus zinc \beta-lactamase the affinity for the second metal ion is low at the pH of crystallization (Kd = 25 mM, 293 K; [Baldwin et al. (1978). Biochem. J. 175, 441–447] and the dissociation constant of the second zinc ion thus apparently decreased at the cryogenic temperature. In addition, the structure of the apo enzyme was determined at 2.5 Å resolution. The removal of the zinc ion by chelating agents causes small changes in the active-site environment.

scholarly journals Hemophagocytic lymphohistiocytosis caused by dominant-negative mutations in STXBP2 that inhibit SNARE-mediated membrane fusion

Blood ◽  
2015 ◽  
Vol 125 (10) ◽  
pp. 1566-1577 ◽  
Author(s):  
Waldo A. Spessott ◽  
Maria L. Sanmillan ◽  
Margaret E. McCormick ◽  
Nishant Patel ◽  
Joyce Villanueva ◽  
...  
Keyword(s):  
Membrane Fusion ◽  
Hemophagocytic Lymphohistiocytosis ◽  
Dominant Negative ◽  
Snare Complex ◽  
Complex Assembly ◽  
Mutant Proteins ◽  
Key Points ◽  
Lymphocyte Cytotoxicity ◽  
Dominant Negative Mutations

Key Points Monoallelic STXBP2 mutations affecting codon 65 impair lymphocyte cytotoxicity and contribute to hemophagocytic lymphohistiocytosis. Munc18-2R65Q/W mutant proteins function in a dominant-negative manner to impair membrane fusion and arrest SNARE-complex assembly.

Dominant-negative mutations in the DNA-binding domain of STAT3 cause hyper-IgE syndrome

Nature ◽  
2007 ◽  
Vol 448 (7157) ◽  
pp. 1058-1062 ◽  
Author(s):  
Yoshiyuki Minegishi ◽  
Masako Saito ◽  
Shigeru Tsuchiya ◽  
Ikuya Tsuge ◽  
Hidetoshi Takada ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Domain ◽  
Dominant Negative ◽  
Dna Binding Domain ◽  
Hyper Ige Syndrome ◽  
Dominant Negative Mutations

The erbA oncogene represses the actions of both retinoid X and retinoid A receptors but does so by distinct mechanisms

1993 ◽  
Vol 13 (10) ◽  
pp. 5970-5980
Author(s):  
H W Chen ◽  
M L Privalsky
Keyword(s):  
Thyroid Hormone ◽  
Hormone Receptors ◽  
Thyroid Hormone Receptor ◽  
Dominant Negative ◽  
Nuclear Hormone Receptors ◽  
Dominant Negative Inhibitor ◽  
Dominant Negative Mutations ◽  
Microbial Systems ◽  
Dna Binding Properties ◽  
Activate Gene

Genetic lesions that function as dominant negative mutations in microbial systems have long been recognized. It is only relatively recently, however, that similar dominant negative mutations have been implicated as a basis for genetic and neoplastic disorders in vertebrates. We describe here a dissection of the actions of the erbA oncogene protein, an aberrant form of thyroid hormone receptor that acts as a dominant negative inhibitor of other nuclear hormone receptors. We demonstrate that the ErbA oncoprotein interferes with thyroid hormone and trans-retinoic acid receptors by competing for binding to the corresponding response elements. Heterodimerization of the ErbA oncoprotein with these receptors does not play an observable role in repression. In contrast, however, the ErbA oncoprotein does efficiently form a heterodimer with the retinoid X receptor (RXR) class of nuclear hormone receptors; complex formation enhances the DNA-binding properties of the ErbA protein but dramatically interferes with the ability of the RXR component to activate gene expression. Our results indicate that the erbA oncogene may play a previously unanticipated role in neoplasia by interfering with RXR function.

scholarly journals Directly repeated insertion of 9-nucleotide sequence detected in penicillin-binding protein 2B gene of penicillin-resistant Streptococcus pneumoniae.

1996 ◽  
Vol 40 (5) ◽  
pp. 1257-1259 ◽  
Author(s):  
A Yamane ◽  
H Nakano ◽  
Y Asahi ◽  
K Ubukata ◽  
M Konno
Keyword(s):  
Streptococcus Pneumoniae ◽  
Nucleotide Sequence ◽  
Molecular Mechanism ◽  
Active Site ◽  
Binding Protein ◽  
Direct Repeat ◽  
Penicillin Binding Protein ◽  
Serine Residue ◽  
Class A ◽  
Class B

We investigated the molecular mechanism of 50 penicillin-resistant Streptococcus pneumoniae strains (penicillin: MIC, > or = 0.125 microgram/ml) having neither class A nor class B mutations in the penicillin-binding protein 2B gene (pbp2b). An analysis of the nucleotide sequences of the pbp2b genes from seven strains revealed an unique direct repeat of 9 nucleotides (TGGTATACT) between active-site serine (residue 385) and Ser-X-Asn (residues 442 to 444) motifs. The same insertion was detected in 13 strains.

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