Crystal structures of bacterial peptidoglycan amidase AmpD and an unprecedented activation mechanism

9 pags, 5 figs, 2 tabsAmpD is a cytoplasmic peptidoglycan (PG) amidase involved in bacterial cell-wall recycling and in induction of β-lactamase, a key enzyme of β-lactam antibiotic resistance. AmpD belongs to the amidase-2 family that includes zinc-dependent amidases and the peptidoglycan-recognition proteins (PGRPs), highly conserved pattern-recognition molecules of the immune system. Crystal structures of Citrobacter freundii AmpD were solved in this study for the apoenzyme, for the holoenzyme at two different pH values, and for the complex with the reaction products, providing insights into the PG recognition and the catalytic process. These structures are significantly different compared with the previously reported NMR structure for the same protein. TheNMRstructure does not possess an accessible active site and shows the protein in what is proposed herein as an inactive "closed" conformation. The transition of the protein from this inactive conformation to the active "open" conformation, as seen in the x-ray structures, was studied by targeted molecular dynamics simulations, which revealed large conformational rearrangements (as much as 17 Å ) in four specific regions representing one-third of the entire protein. It is proposed that the large conformational change that would take the inactive NMR structure to the active x-ray structure represents an unprecedented mechanism for activation of AmpD. Analysis is presented to argue that this activation mechanism might be representative of a regulatory process for other intracellular members of the bacterial amidase-2 family of enzymes. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.This work was supported, in whole or in part, by the National Institutes of Health. This work was also supported by grants from the Spanish Ministry of Science and Technology (BFU2008-01711), EU-CP223111 (CARE-PNEUMO, European Union), and the COMBACT program (S-BIO-0260/2006). We acknowledge the Spanish Ministerio de Ciencia e Innovación (PI201060E013) and Consejo Superior de Investigaciones Científicas for financial support and for provision of synchrotron radiation facilitie

How allosteric control of Staphylococcus aureus penicillin binding protein 2a enables methicillin resistance and physiological function

6 pags, 4 figs, 1 tabThe expression of penicillin binding protein 2a (PBP2a) is the basis for the broad clinical resistance to the β-lactam antibiotics by methicillin-resistant Staphylococcus aureus (MRSA). The highmolecular mass penicillin binding proteins of bacteria catalyze in separate domains the transglycosylase and transpeptidase activities required for the biosynthesis of the peptidoglycan polymer that comprises the bacterial cell wall. In bacteria susceptible to β-lactam antibiotics, the transpeptidase activity of their penicillin binding proteins (PBPs) is lost as a result of irreversible acylation of an active site serine by the β-lactam antibiotics. In contrast, the PBP2a of MRSA is resistant to β-lactam acylation and successfully catalyzes the DD-transpeptidation reaction necessary to complete the cell wall. The inability to contain MRSA infection with β-lactam antibiotics is a continuing public health concern. We report herein the identification of an allosteric binding domain - a remarkable 60 Å distant from the DD-transpeptidase active site - discovered by crystallographic analysis of a soluble construct of PBP2a. When this allosteric site is occupied, a multiresidue conformational change culminates in the opening of the active site to permit substrate entry. This same crystallographic analysis also reveals the identity of three allosteric ligands: muramic acid (a saccharide component of the peptidoglycan), the cell wall peptidoglycan, and ceftaroline, a recently approved anti-MRSA β-lactam antibiotic. The ability of an anti-MRSA β-lactam antibiotic to stimulate allosteric opening of the active site, thus predisposing PBP2a to inactivation by a second β-lactam molecule, opens an unprecedented realm for β-lactam antibiotic structure-based design.Work in the United States was supported by National Institutes of Health Grants AI090818 and AI104987, and work in Spain was supported by Grants BFU2011-25326 (from the Spanish Ministry of Economy and Competitiveness) and S2010/BMD-2457 (from the Autonomous Government of Madrid)

How Allosteric Control of Staphylococcus aureus Penicillin-Binding Protein 2a Enables Methicillin-Resistance and Physiological Function

The expression of penicillin binding protein 2a (PBP2a) is the basis for the broad clinical resistance to the β-lactam antibiotics by methicillin-resistant Staphylococcus aureus (MRSA). The highmolecular mass penicillin binding proteins of bacteria catalyze in separate domains the transglycosylase and transpeptidase activities required for the biosynthesis of the peptidoglycan polymer that comprises the bacterial cell wall. In bacteria susceptible to β-lactam antibiotics, the transpeptidase activity of their penicillin binding proteins (PBPs) is lost as a result of irreversible acylation of an active site serine by the β-lactam antibiotics. In contrast, the PBP2a of MRSA is resistant to β-lactam acylation and successfully catalyzes the DD-transpeptidation reaction necessary to complete the cell wall. The inability to contain MRSA infection with β-lactam antibiotics is a continuing public health concern. We report herein the identification of an allosteric binding domain - a remarkable 60 Å distant from the DD-transpeptidase active site - discovered by crystallographic analysis of a soluble construct of PBP2a. When this allosteric site is occupied, a multiresidue conformational change culminates in the opening of the active site to permit substrate entry. This same crystallographic analysis also reveals the identity of three allosteric ligands: muramic acid (a saccharide component of the peptidoglycan), the cell wall peptidoglycan, and ceftaroline, a recently approved anti-MRSA β-lactam antibiotic. The ability of an anti-MRSA β-lactam antibiotic to stimulate allosteric opening of the active site, thus predisposing PBP2a to inactivation by a second β-lactam molecule, opens an unprecedented realm for β-lactam antibiotic structure-based design.Fil: Otero, Lisandro Horacio. Consejo Superior de Investigaciones Científicas. Instituto de Química Física; España. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Rojas Altuve, Alzoray. Consejo Superior de Investigaciones Científicas. Instituto de Química Física; EspañaFil: Llarrull, Leticia Irene. University of Notre Dame; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Rosario. Instituto de Biología Molecular y Celular de Rosario. Universidad Nacional de Rosario. Facultad de Ciencias Bioquímicas y Farmacéuticas. Instituto de Biología Molecular y Celular de Rosario; ArgentinaFil: Carrasco López, Cesar. Consejo Superior de Investigaciones Científicas. Instituto de Química Física; EspañaFil: Kumarasiri, Malika. University of Notre Dame; Estados UnidosFil: Lastochkin, Elena. University of Notre Dame; Estados UnidosFil: Fishovitz, Jennifer. University of Notre Dame; Estados UnidosFil: Dawley, Matthew. University of Notre Dame; Estados UnidosFil: Hesek, Dusan. University of Notre Dame; Estados UnidosFil: Lee, Mijoon. University of Notre Dame; Estados UnidosFil: Johnson, Jarrod W.. University of Notre Dame; Estados UnidosFil: Fisher, Jed F.. University of Notre Dame; Estados UnidosFil: Chang, Mayland. University of Notre Dame; Estados UnidosFil: Mobashery, Shahriar. University of Notre Dame; Estados UnidosFil: Hermoso, Juan A.. Consejo Superior de Investigaciones Científicas. Instituto de Química Física; Españ

Structural characterization of PaaX, the main repressor of the phenylacetate degradation pathway in Escherichia coli W: A novel fold of transcription regulator proteins

15 p.-8 fig.-2 tab.PaaX is a transcriptional repressor of the phenylacetic acid (PAA) catabolic pathway, a central route for bacterial aerobic degradation of aromatic compounds. Induction of the route is achieved through the release of PaaX from its promoter sequences by the first compound of the pathway, phenylacetyl-coenzyme A (PA-CoA). We report the crystal structure of PaaX from Escherichia coli W. PaaX displays a novel type of fold for transcription regulators, showing a dimeric conformation where the monomers present a three-domain structure: an N-terminal winged helix-turn-helix domain, a dimerization domain similar to the Cas2 protein and a C-terminal domain without structural homologs. The domains are separated by a crevice amenable to harbour a PA-CoA molecule. The biophysical characterization of the protein in solution confirmed several hints predicted from the structure, i.e. its dimeric conformation, a modest importance of cysteines and a high dependence of solubility and thermostability on ionic strength. At a moderately acidic pH, the protein formed a stable folding intermediate with remaining α-helical structure, a disrupted tertiary structure and exposed hydrophobic patches. Our results provide valuable information to understand the stability and mechanism of PaaX and pave the way for further analysis of other regulators with similar structural configurations.This research was funded by the following sources: Grants PID2019-105126RB-I00, PID2022-139209OB-C21 (MCIN/AEI/10.13039/501100011033/and ERDF A way of making Europe), TED2021-129747B-C22 (AEI/10.13039/501100011033/NextGenerationEU/PRTR) and CIBER-Consorcio Centro de Investigación Biomédica en Red (CIBERES, Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación, Spain) to JMS; grants PID2020-115331GB-100 funded by MCIN/AEI/10.13039/501100011033 and CRSII5_198737/1 (Swiss National Science Foundation) to JAH; grant PID2021-128751NB-I00 (MICINN/AEI/FEDER/UE) to IU, and grant RYC2021-030916-I by the Spanish Agencia Estatal de Investigación to RM. VMH-R was supported by a FPU PhD fellowship from Spanish Ministerio de Educación y Ciencia.Peer reviewe

Crystallization and preliminary X-ray diffraction studies of the transcriptional repressor PaaX, the main regulator of the phenylacetic acid degradation pathway in Escherichia coli W

3 p.-2 fig.-1 tab.PaaX is the main regulator of the phenylacetic acid aerobic degradation pathway in bacteria and acts as a transcriptional repressor in the absence of its inducer phenylacetyl-coenzyme A. The natural presence and the recent accumulation of a variety of highly toxic aromatic compounds owing to human pollution has created considerable interest in the study of degradation pathways in bacteria, the most important microorganisms capable of recycling these compounds, in order to design and apply novel bioremediation strategies. PaaX from Escherichia coliWwas cloned, overexpressed, purified and crystallized using the sitting-drop vapour-diffusion method at 291 K. Crystals grew from a mixture of 0.9 MLi2SO4 and 0.5 Msodium citrate pH 5.8. These crystals, which belonged to the monoclinic space group C2 with unit-cell parameters a = 167.88, b = 106.23, c = 85.87 A ° , = 108.33 , allowed the collection of an X-ray data set to 2.3 A ° resolution.This work was supported by grants BIO2003-05309-C04-04, BFU2005-01645 and BIO2007-67304-C02-02 from the Spanish Ministry of Science. This is a product of the ‘Factoría Española de Cristalización’ Ingenio/Consolider 2010 project.Peer reviewe

Incidence of marginal ulcer 1 month and 1 to 2 years after gastric bypass: A prospective consecutive endoscopic evaluation of 442 patients with morbid obesity

Background: Marginal ulcer (MU) is an occasional complication after gastric bypass. We studied the incidence of this complication by a prospective routine endoscopic evaluation. 441 morbidly obese patients were studied prospectively. There were 358 women and 97 men, with mean age 41 years and mean BMI 43 kg/m2. An endoscopic evaluation was performed in all 1 month after surgery, which was repeated in 315 patients (71%) 17 months after surgery, independent of the presence or absence of symptoms. Patients were submitted either to laparotomic resectional gastric bypass (360 patients), employing a circularstapler-25 or to laparoscopic gastric bypass (81 patients), in whom a hand-sewn anastomosis was performed. One month after surgery, 15 patients (4.1%) of the 360 laparotomic gastric bypass and 10 (12.3%) of the 81 laparoscopic gastric bypass presented an "early" marginal ulcer (p∈<∈0.02). Seven patients among the 25 with MU were asymptomatic (28%). Endoscopy was repeated 17 months after

LIGADURA QUIRÚRGICA DE VASOS ARTERIALES CERVICALES EN SITUACIONES DE EMERGENCIA

Se evaluaron cuarenta pacientes a quienes se les aplico ligadura quirúrgica de los vasos arteriales cervicales  como medida hemostática en situación de emergencia. De acuerdo a la causa del sangramiento, treinta fueron por patología neoplásica, dos epistaxis por hipertensión arterial sistémica, otros dos posterior a tonsilectomía y seis por traumatismo cervical penetrante. La ligadura de la arteria carótida externa fue el principal procedimiento hemostático en los tres primeros grupos.  El 22,5% de la serie ingreso con signos de shock hipovolémico. Del grupo oncológico, el 13,33%  requirió un nuevo ingreso a quirófano por resangramiento y el 30%  sobrevivió más de un año posterior al procedimiento. La crisis sanitaria, la cuarentena por COVID-19 y la evolución hacia lesiones traumáticas más extensas han determinado la aplicación inmediata del procedimiento descrito como una alternativa hemostática viable, rápida y segura  en situación de urgencia

Crystal structures of bacterial peptidoglycan amidase AmpD and an unprecedented activation mechanism.

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Binding of non-canonical peptidoglycan controls Vibrio cholerae broad spectrum racemase activity

Broad-spectrum amino acid racemases (Bsrs) enable bacteria to generate non-canonical D-amino acids (NCDAAs), whose roles and impact on microbial physiology, including modulation of cell wall structure and dissolution of biofilms, are just beginning to be appreciated. Here we used a diverse array of structural, biochemical and molecular simulation studies to define and characterize how BsrV is post-translationally regulated. We discovered that contrary to Vibrio cholerae alanine racemase AlrV highly compacted active site, BsrV’s is broader and can be occupied by cell wall stem peptides. We found that peptidoglycan peptides modified with NCDAAs are better stabilized by BsrV’s catalytic cavity and show better inhibitory capacity than canonical muropeptides. Notably, BsrV binding and inhibition can be recapitulated by undigested peptidoglycan sacculi as it exists in the cell. Docking simulations of BsrV binding the peptidoglycan polymer generate a model where the peptide stems are perfectly accommodated and stabilized within each of the dimeŕs active sites. Taking these biochemical and structural data together, we propose that inhibition of BsrV by peptidoglycan peptides underlies a negative regulatory mechanism to avoid excessive NCDAA production. Our results collectively open the door to use “à la carte” synthetic peptides as a tool to modulate DAAs production of Bsr enzymes