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1.
J Biol Chem ; 299(3): 102936, 2023 03.
Artículo en Inglés | MEDLINE | ID: mdl-36702253

RESUMEN

Staphylococcus aureus and Staphylococcus epidermidis are frequently associated with medical device infections that involve establishment of a bacterial biofilm on the device surface. Staphylococcal surface proteins Aap, SasG, and Pls are members of the Periscope Protein class and have been implicated in biofilm formation and host colonization; they comprise a repetitive region ("B region") and an N-terminal host colonization domain within the "A region," predicted to be a lectin domain. Repetitive E-G5 domains (as found in Aap, SasG, and Pls) form elongated "stalks" that would vary in length with repeat number, resulting in projection of the N-terminal A domain variable distances from the bacterial cell surface. Here, we present the structures of the lectin domains within A regions of SasG, Aap, and Pls and a structure of the Aap lectin domain attached to contiguous E-G5 repeats, suggesting the lectin domains will sit at the tip of the variable length rod. We demonstrate that these isolated domains (Aap, SasG) are sufficient to bind to human host desquamated nasal epithelial cells. Previously, proteolytic cleavage or a deletion within the A domain had been reported to induce biofilm formation; the structures suggest a potential link between these observations. Intriguingly, while the Aap, SasG, and Pls lectin domains bind a metal ion, they lack the nonproline cis peptide bond thought to be key for carbohydrate binding by the lectin fold. This suggestion of noncanonical ligand binding should be a key consideration when investigating the host cell interactions of these bacterial surface proteins.


Asunto(s)
Proteínas Bacterianas , Modelos Moleculares , Dominios Proteicos , Staphylococcus aureus , Humanos , Adhesinas Bacterianas/genética , Adhesinas Bacterianas/metabolismo , Proteínas Bacterianas/química , Proteínas Bacterianas/metabolismo , Lectinas/química , Lectinas/metabolismo , Infecciones Estafilocócicas/microbiología , Staphylococcus epidermidis/química , Staphylococcus epidermidis/genética , Staphylococcus epidermidis/metabolismo , Dominios Proteicos/fisiología , Estructura Terciaria de Proteína , Unión Proteica , Staphylococcus aureus/química , Staphylococcus aureus/genética , Staphylococcus aureus/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Escherichia coli , Células Epiteliales/microbiología
2.
Microbiology (Reading) ; 168(12)2022 12.
Artículo en Inglés | MEDLINE | ID: mdl-36748525

RESUMEN

Peptide transporters play important nutritional and cell signalling roles in Bacillus subtilis, which are pronounced during stationary phase adaptations and development. Three high-affinity ATP-binding cassette (ABC) family transporters are involved in peptide uptake - the oligopeptide permease (Opp), another peptide permease (App) and a less well-characterized dipeptide permease (Dpp). Here we report crystal structures of the extracellular substrate binding proteins, OppA and DppE, which serve the Opp and Dpp systems, respectively. The structure of OppA was determined in complex with endogenous peptides, modelled as Ser-Asn-Ser-Ser, and with the sporulation-promoting peptide Ser-Arg-Asn-Val-Thr, which bind with K d values of 0.4 and 2 µM, respectively, as measured by isothermal titration calorimetry. Differential scanning fluorescence experiments with a wider panel of ligands showed that OppA has highest affinity for tetra- and penta-peptides. The structure of DppE revealed the unexpected presence of a murein tripeptide (MTP) ligand, l-Ala-d-Glu-meso-DAP, in the peptide binding groove. The mode of MTP binding in DppE is different to that observed in the murein peptide binding protein, MppA, from Escherichia coli, suggesting independent evolution of these proteins from an OppA-like precursor. The presence of MTP in DppE points to a role for Dpp in the uptake and recycling of cell wall peptides, a conclusion that is supported by analysis of the genomic context of dpp, which revealed adjacent genes encoding enzymes involved in muropeptide catabolism in a gene organization that is widely conserved in Firmicutes.


Asunto(s)
Bacillus subtilis , Peptidoglicano , Bacillus subtilis/genética , Bacillus subtilis/metabolismo , Peptidoglicano/metabolismo , Proteínas Bacterianas/metabolismo , Oligopéptidos , Proteínas de Transporte de Membrana/metabolismo , Escherichia coli/genética , Transportadoras de Casetes de Unión a ATP/genética , Transportadoras de Casetes de Unión a ATP/metabolismo
3.
Proc Natl Acad Sci U S A ; 116(52): 26540-26548, 2019 Dec 26.
Artículo en Inglés | MEDLINE | ID: mdl-31818940

RESUMEN

Streptococcus groups A and B cause serious infections, including early onset sepsis and meningitis in newborns. Rib domain-containing surface proteins are found associated with invasive strains and elicit protective immunity in animal models. Yet, despite their apparent importance in infection, the structure of the Rib domain was previously unknown. Structures of single Rib domains of differing length reveal a rare case of domain atrophy through deletion of 2 core antiparallel strands, resulting in the loss of an entire sheet of the ß-sandwich from an immunoglobulin-like fold. Previously, observed variation in the number of Rib domains within these bacterial cell wall-attached proteins has been suggested as a mechanism of immune evasion. Here, the structure of tandem domains, combined with molecular dynamics simulations and small angle X-ray scattering, suggests that variability in Rib domain number would result in differential projection of an N-terminal host-colonization domain from the bacterial surface. The identification of 2 further structures where the typical B-D-E immunoglobulin ß-sheet is replaced with an α-helix further confirms the extensive structural malleability of the Rib domain.

4.
J Am Chem Soc ; 141(40): 15818-15826, 2019 10 09.
Artículo en Inglés | MEDLINE | ID: mdl-31518131

RESUMEN

Solvent organization is a key but underexploited contributor to the thermodynamics of protein-ligand recognition, with implications for ligand discovery, drug resistance, and protein engineering. Here, we explore the contribution of solvent to ligand binding in the Haemophilus influenzae virulence protein SiaP. By introducing a single mutation without direct ligand contacts, we observed a >1000-fold change in sialic acid binding affinity. Crystallographic and calorimetric data of wild-type and mutant SiaP showed that this change results from an enthalpically unfavorable perturbation of the solvent network. This disruption is reflected by changes in the normalized atomic displacement parameters of crystallographic water molecules. In SiaP's enclosed cavity, relative differences in water-network dynamics serve as a simple predictor of changes in the free energy of binding upon changing protein, ligand, or both. This suggests that solvent structure is an evolutionary constraint on protein sequence that contributes to ligand affinity and selectivity.


Asunto(s)
Solventes/química , Proteínas Virales/química , Factores de Virulencia/química , Agua/química , Sitios de Unión , Ligandos , Unión Proteica , Conformación Proteica , Termodinámica
5.
Nat Chem Biol ; 13(3): 275-281, 2017 03.
Artículo en Inglés | MEDLINE | ID: mdl-28068311

RESUMEN

The asymmetric dehydration of alcohols is an important process for the direct synthesis of alkenes. We report the structure and substrate specificity of the bifunctional linalool dehydratase isomerase (LinD) from the bacterium Castellaniella defragrans that catalyzes in nature the hydration of ß-myrcene to linalool and the subsequent isomerization to geraniol. Enzymatic kinetic resolutions of truncated and elongated aromatic and aliphatic tertiary alcohols (C5-C15) that contain a specific signature motif demonstrate the broad substrate specificity of LinD. The three-dimensional structure of LinD from Castellaniella defragrans revealed a pentamer with active sites at the protomer interfaces. Furthermore, the structure of LinD in complex with the product geraniol provides initial mechanistic insights into this bifunctional enzyme. Site-directed mutagenesis confirmed active site amino acid residues essential for its dehydration and isomerization activity. These structural and mechanistic insights facilitate the development of hydrating catalysts, enriching the toolbox for novel bond-forming biocatalysis.


Asunto(s)
Alcoholes/química , Alcoholes/metabolismo , Hidroliasas/metabolismo , Biocatálisis , Deshidratación , Estructura Molecular
6.
Proc Natl Acad Sci U S A ; 113(21): 5850-5, 2016 May 24.
Artículo en Inglés | MEDLINE | ID: mdl-27162326

RESUMEN

To acquire essential Fe(III), bacteria produce and secrete siderophores with high affinity and selectivity for Fe(III) to mediate its uptake into the cell. Here, we show that the periplasmic binding protein CeuE of Campylobacter jejuni, which was previously thought to bind the Fe(III) complex of the hexadentate siderophore enterobactin (Kd ∼ 0.4 ± 0.1 µM), preferentially binds the Fe(III) complex of the tetradentate enterobactin hydrolysis product bis(2,3-dihydroxybenzoyl-l-Ser) (H5-bisDHBS) (Kd = 10.1 ± 3.8 nM). The protein selects Λ-configured [Fe(bisDHBS)](2-) from a pool of diastereomeric Fe(III)-bisDHBS species that includes complexes with metal-to-ligand ratios of 1:1 and 2:3. Cocrystal structures show that, in addition to electrostatic interactions and hydrogen bonding, [Fe(bisDHBS)](2-) binds through coordination of His227 and Tyr288 to the iron center. Similar binding is observed for the Fe(III) complex of the bidentate hydrolysis product 2,3-dihydroxybenzoyl-l-Ser, [Fe(monoDHBS)2](3-) The mutation of His227 and Tyr288 to noncoordinating residues (H227L/Y288F) resulted in a substantial loss of affinity for [Fe(bisDHBS)](2-) (Kd ∼ 0.5 ± 0.2 µM). These results suggest a previously unidentified role for CeuE within the Fe(III) uptake system of C. jejuni, provide a molecular-level understanding of the underlying binding pocket adaptations, and rationalize reports on the use of enterobactin hydrolysis products by C. jejuni, Vibrio cholerae, and other bacteria with homologous periplasmic binding proteins.


Asunto(s)
Proteínas Bacterianas/química , Campylobacter jejuni/metabolismo , Proteínas Portadoras/química , Complejos de Coordinación/química , Enterobactina/metabolismo , Hierro/metabolismo , Sideróforos/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Benzoatos/química , Benzoatos/metabolismo , Campylobacter jejuni/genética , Proteínas Portadoras/genética , Proteínas Portadoras/metabolismo , Complejos de Coordinación/metabolismo , Cristalografía por Rayos X , Expresión Génica , Hidrazonas/química , Hidrazonas/metabolismo , Enlace de Hidrógeno , Hidrólisis , Transporte Iónico , Proteínas de Unión a Hierro , Ligandos , Modelos Moleculares , Mutación , Unión Proteica , Electricidad Estática , Estereoisomerismo
7.
Int J Mol Sci ; 20(22)2019 Nov 06.
Artículo en Inglés | MEDLINE | ID: mdl-31698762

RESUMEN

Muramidases/lysozymes are important bio-molecules, which cleave the glycan backbone in the peptidoglycan polymer found in bacterial cell walls. The glycoside hydrolase (GH) family 22 C-type lysozyme, from the folivorous bird Opisthocomus hoazin (stinkbird), was expressed in Aspergillus oryzae, and a set of variants was produced. All variants were enzymatically active, including those designed to probe key differences between the Hoatzin enzyme and Hen Egg White lysozyme. Four variants showed improved thermostability at pH 4.7, compared to the wild type. The X-ray structure of the enzyme was determined in the apo form and in complex with chitin oligomers. Bioinformatic analysis of avian GH22 amino acid sequences showed that they separate out into three distinct subgroups (chicken-like birds, sea birds and other birds). The Hoatzin is found in the "other birds" group and we propose that this represents a new cluster of avian upper-gut enzymes.


Asunto(s)
Aves/metabolismo , Muramidasa/química , Tracto Gastrointestinal Superior/enzimología , Secuencia de Aminoácidos , Animales , Aspergillus/metabolismo , Pared Celular/metabolismo , Concentración de Iones de Hidrógeno , Modelos Moleculares , Filogenia , Polisacáridos/química , Electricidad Estática
8.
Int J Mol Sci ; 20(19)2019 Oct 03.
Artículo en Inglés | MEDLINE | ID: mdl-31623309

RESUMEN

Amylases are probably the best studied glycoside hydrolases and have a huge biotechnological value for industrial processes on starch. Multiple amylases from fungi and microbes are currently in use. Whereas bacterial amylases are well suited for many industrial processes due to their high stability, fungal amylases are recognized as safe and are preferred in the food industry, although they lack the pH tolerance and stability of their bacterial counterparts. Here, we describe three amylases, two of which have a broad pH spectrum extending to pH 8 and higher stability well suited for a broad set of industrial applications. These enzymes have the characteristic GH13 α-amylase fold with a central (ß/α)8-domain, an insertion domain with the canonical calcium binding site and a C-terminal ß-sandwich domain. The active site was identified based on the binding of the inhibitor acarbose in form of a transglycosylation product, in the amylases from Thamnidium elegans and Cordyceps farinosa. The three amylases have shortened loops flanking the nonreducing end of the substrate binding cleft, creating a more open crevice. Moreover, a potential novel binding site in the C-terminal domain of the Cordyceps enzyme was identified, which might be part of a starch interaction site. In addition, Cordyceps farinosa amylase presented a successful example of using the microseed matrix screening technique to significantly speed-up crystallization.


Asunto(s)
Amilasas/química , Amilasas/metabolismo , Hongos/enzimología , Sitios de Unión , Dominio Catalítico , Activación Enzimática , Estabilidad de Enzimas , Glucosa/química , Glucosa/metabolismo , Glicosilación , Concentración de Iones de Hidrógeno , Modelos Moleculares , Conformación Molecular , Unión Proteica , Relación Estructura-Actividad , alfa-Amilasas/química , alfa-Amilasas/metabolismo
9.
J Biol Chem ; 292(20): 8342-8355, 2017 05 19.
Artículo en Inglés | MEDLINE | ID: mdl-28348075

RESUMEN

Human insulin is a pivotal protein hormone controlling metabolism, growth, and aging and whose malfunctioning underlies diabetes, some cancers, and neurodegeneration. Despite its central position in human physiology, the in vivo oligomeric state and conformation of insulin in its storage granules in the pancreas are not known. In contrast, many in vitro structures of hexamers of this hormone are available and fall into three conformational states: T6, T3Rf3, and R6 As there is strong evidence for accumulation of neurotransmitters, such as serotonin and dopamine, in insulin storage granules in pancreatic ß-cells, we probed by molecular dynamics (MD) and protein crystallography (PC) if these endogenous ligands affect and stabilize insulin oligomers. Parallel studies independently converged on the observation that serotonin binds well within the insulin hexamer (site I), stabilizing it in the T3R3 conformation. Both methods indicated serotonin binding on the hexamer surface (site III) as well. MD, but not PC, indicated that dopamine was also a good site III ligand. Some of the PC studies also included arginine, which may be abundant in insulin granules upon processing of pro-insulin, and stable T3R3 hexamers loaded with both serotonin and arginine were obtained. The MD and PC results were supported further by in solution spectroscopic studies with R-state-specific chromophore. Our results indicate that the T3R3 oligomer is a plausible insulin pancreatic storage form, resulting from its complex interplay with neurotransmitters, and pro-insulin processing products. These findings may have implications for clinical insulin formulations.


Asunto(s)
Simulación por Computador , Células Secretoras de Insulina , Insulina , Modelos Biológicos , Neurotransmisores/metabolismo , Multimerización de Proteína , Vesículas Secretoras , Serotonina/metabolismo , Humanos , Insulina/química , Insulina/metabolismo , Células Secretoras de Insulina/química , Células Secretoras de Insulina/metabolismo , Simulación de Dinámica Molecular , Vesículas Secretoras/química , Vesículas Secretoras/metabolismo
10.
J Biol Chem ; 289(18): 12842-51, 2014 May 02.
Artículo en Inglés | MEDLINE | ID: mdl-24627488

RESUMEN

The adjacent fibrinogen (Fg)- and fibronectin (Fn)-binding sites on Fn-binding protein A (FnBPA), a cell surface protein from Staphylococcus aureus, are implicated in the initiation and persistence of infection. FnBPA contains a single Fg-binding site (that also binds elastin) and multiple Fn-binding sites. Here, we solved the structure of the N2N3 domains containing the Fg-binding site of FnBPA in the apo form and in complex with a Fg peptide. The Fg binding mechanism is similar to that of homologous bacterial proteins but without the requirement for "latch" strand residues. We show that the Fg-binding sites and the most N-terminal Fn-binding sites are nonoverlapping but in close proximity. Although Fg and a subdomain of Fn can form a ternary complex on an FnBPA protein construct containing a Fg-binding site and single Fn-binding site, binding of intact Fn appears to inhibit Fg binding, suggesting steric regulation. Given the concentrations of Fn and Fg in the plasma, this mechanism might result in targeting of S. aureus to fibrin-rich thrombi or elastin-rich tissues.


Asunto(s)
Adhesinas Bacterianas/metabolismo , Fibrinógeno/metabolismo , Fibronectinas/metabolismo , Staphylococcus aureus/metabolismo , Adhesinas Bacterianas/química , Adhesinas Bacterianas/genética , Secuencia de Aminoácidos , Sitios de Unión , Cristalografía por Rayos X , Fibrinógeno/química , Fibronectinas/química , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Péptidos/química , Péptidos/metabolismo , Unión Proteica , Estructura Secundaria de Proteína , Estructura Terciaria de Proteína , Staphylococcus aureus/genética , Resonancia por Plasmón de Superficie
11.
Acta Crystallogr D Biol Crystallogr ; 71(Pt 2): 408-15, 2015 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-25664752

RESUMEN

The large bowel microbiota, a complex ecosystem resident within the gastrointestinal tract of all human beings and large mammals, functions as an essential, nonsomatic metabolic organ, hydrolysing complex dietary polysaccharides and modulating the host immune system to adequately tolerate ingested antigens. A significant member of this community, Bacteroides thetaiotaomicron, has evolved a complex system for sensing and processing a wide variety of natural glycoproducts in such a way as to provide maximum benefit to itself, the wider microbial community and the host. The immense ability of B. thetaiotaomicron as a `glycan specialist' resides in its enormous array of carbohydrate-active enzymes, many of which are arranged into polysaccharide-utilization loci (PULs) that are able to degrade sugar polymers that are often inaccessible to other gut residents, notably α-mannan. The B. thetaiotaomicron genome encodes ten putative α-mannanases spread across various PULs; however, little is known about the activity of these enzymes or the wider implications of α-mannan metabolism for the health of both the microbiota and the host. In this study, SAD phasing of a selenomethionine derivative has been used to investigate the structure of one such B. thetaiotaomicron enzyme, BT2949, which belongs to the GH76 family of α-mannanases. BT2949 presents a classical (α/α)6-barrel structure comprising a large extended surface cleft common to other GH76 family members. Analysis of the structure in conjunction with sequence alignments reveals the likely location of the catalytic active site of this noncanonical GH76.


Asunto(s)
Proteínas Bacterianas/química , Bacteroides/química , Glicósido Hidrolasas/química , Secuencia de Aminoácidos , Infecciones por Bacteroides/microbiología , Cristalografía por Rayos X , Tracto Gastrointestinal/microbiología , Humanos , Modelos Moleculares , Datos de Secuencia Molecular , Conformación Proteica , Alineación de Secuencia
12.
Mol Microbiol ; 93(5): 975-91, 2014 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-25041308

RESUMEN

Chromosome copy number in cells is controlled so that the frequency of initiation of DNA replication matches that of cell division. In bacteria, this is achieved through regulation of the interaction between the initiator protein DnaA and specific DNA elements arrayed at the origin of replication. DnaA assembles at the origin and promotes DNA unwinding and the assembly of a replication initiation complex. SirA is a DnaA-interacting protein that inhibits initiation of replication in diploid Bacillus subtilis cells committed to the developmental pathway leading to formation of a dormant spore. Here we present the crystal structure of SirA in complex with the N-terminal domain of DnaA revealing a heterodimeric complex. The interacting surfaces of both proteins are α-helical with predominantly apolar side-chains packing in a hydrophobic interface. Site-directed mutagenesis experiments confirm the importance of this interface for the interaction of the two proteins in vitro and in vivo. Localization of GFP-SirA indicates that the protein accumulates at the replisome in sporulating cells, likely through a direct interaction with DnaA. The SirA interacting surface of DnaA corresponds closely to the HobA-interacting surface of DnaA from Helicobacter pylori even though HobA is an activator of DnaA and SirA is an inhibitor.


Asunto(s)
Bacillus subtilis/metabolismo , Proteínas Bacterianas/metabolismo , Replicación del ADN , Proteínas de Unión al ADN/metabolismo , Esporas Bacterianas/metabolismo , Bacillus subtilis/genética , Bacillus subtilis/crecimiento & desarrollo , Proteínas Bacterianas/genética , Proteínas de Unión al ADN/genética , Unión Proteica , Estructura Terciaria de Proteína , Esporas Bacterianas/genética , Esporas Bacterianas/crecimiento & desarrollo
13.
Chembiochem ; 16(7): 1052-9, 2015 May 04.
Artículo en Inglés | MEDLINE | ID: mdl-25809902

RESUMEN

Oxidoreductases from Streptomyces sp. GF3546 [3546-IRED], Bacillus cereus BAG3X2 (BcIRED) and Nocardiopsis halophila (NhIRED) each reduce prochiral 2-methylpyrroline (2MPN) to (S)-2-methylpyrrolidine with >95 % ee and also a number of other imine substrates with good selectivity. Structures of BcIRED and NhIRED have helped to identify conserved active site residues within this subgroup of imine reductases that have S selectivity towards 2MPN, including a tyrosine residue that has a possible role in catalysis and superimposes with an aspartate in related enzymes that display R selectivity towards the same substrate. Mutation of this tyrosine residue-Tyr169-in 3546-IRED to Phe resulted in a mutant of negligible activity. The data together provide structural evidence for the location and significance of the Tyr residue in this group of imine reductases, and permit a comparison of the active sites of enzymes that reduce 2MPN with either R or S selectivity.


Asunto(s)
Biocatálisis , Iminas/química , Iminas/metabolismo , NADH NADPH Oxidorreductasas/química , NADH NADPH Oxidorreductasas/metabolismo , Pirrolidinas/química , Pirrolidinas/metabolismo , Dominio Catalítico , Bacterias Grampositivas/enzimología , Modelos Moleculares , Oxidación-Reducción , Homología de Secuencia de Aminoácido , Especificidad por Sustrato
14.
Chembiochem ; 16(6): 968-76, 2015 Apr 13.
Artículo en Inglés | MEDLINE | ID: mdl-25737306

RESUMEN

The FAD-dependent monooxygenase HbpA from Pseudomonas azelaica HBP1 catalyses the hydroxylation of 2-hydroxybiphenyl (2HBP) to 2,3-dihydroxybiphenyl (23DHBP). HbpA has been used extensively as a model for studying flavoprotein hydroxylases under process conditions, and has also been subjected to directed-evolution experiments that altered its catalytic properties. The structure of HbpA has been determined in its apo and FAD-complex forms to resolutions of 2.76 and 2.03 Å, respectively. Comparisons of the HbpA structure with those of homologues, in conjunction with a model of the reaction product in the active site, reveal His48 as the most likely acid/base residue to be involved in the hydroxylation mechanism. Mutation of His48 to Ala resulted in an inactive enzyme. The structures of HbpA also provide evidence that mutants achieved by directed evolution that altered activity are comparatively remote from the substrate-binding site.


Asunto(s)
Apoenzimas/química , Apoenzimas/metabolismo , Dominio Catalítico , Evolución Molecular Dirigida , Flavina-Adenina Dinucleótido/metabolismo , Oxigenasas de Función Mixta/química , Oxigenasas de Función Mixta/metabolismo , Apoenzimas/genética , Compuestos de Bifenilo/metabolismo , Hidroxilación , Oxigenasas de Función Mixta/genética , NAD/metabolismo , Multimerización de Proteína , Estructura Cuaternaria de Proteína , Pseudomonas/enzimología , Homología de Secuencia de Aminoácido
15.
Proc Natl Acad Sci U S A ; 109(17): E1011-8, 2012 Apr 24.
Artículo en Inglés | MEDLINE | ID: mdl-22493247

RESUMEN

Staphylococcus aureus and Staphylococcus epidermidis form communities (called biofilms) on inserted medical devices, leading to infections that affect many millions of patients worldwide and cause substantial morbidity and mortality. As biofilms are resistant to antibiotics, device removal is often required to resolve the infection. Thus, there is a need for new therapeutic strategies and molecular data that might assist their development. Surface proteins S. aureus surface protein G (SasG) and accumulation-associated protein (S. epidermidis) promote biofilm formation through their "B" regions. B regions contain tandemly arrayed G5 domains interspersed with approximately 50 residue sequences (herein called E) and have been proposed to mediate intercellular accumulation through Zn(2+)-mediated homodimerization. Although E regions are predicted to be unstructured, SasG and accumulation-associated protein form extended fibrils on the bacterial surface. Here we report structures of E-G5 and G5-E-G5 from SasG and biophysical characteristics of single and multidomain fragments. E sequences fold cooperatively and form interlocking interfaces with G5 domains in a head-to-tail fashion, resulting in a contiguous, elongated, monomeric structure. E and G5 domains lack a compact hydrophobic core, and yet G5 domain and multidomain constructs have thermodynamic stabilities only slightly lower than globular proteins of similar size. Zn(2+) does not cause SasG domains to form dimers. The work reveals a paradigm for formation of fibrils on the 100-nm scale and suggests that biofilm accumulation occurs through a mechanism distinct from the "zinc zipper." Finally, formation of two domains by each repeat (as in SasG) might reduce misfolding in proteins when the tandem arrangement of highly similar sequences is advantageous.


Asunto(s)
Proteínas Bacterianas/química , Biopelículas , Staphylococcus aureus/metabolismo , Staphylococcus epidermidis/metabolismo , Secuencia de Aminoácidos , Proteínas Bacterianas/metabolismo , Dimerización , Datos de Secuencia Molecular , Pliegue de Proteína , Termodinámica
16.
Biochemistry ; 53(21): 3392-402, 2014 Jun 03.
Artículo en Inglés | MEDLINE | ID: mdl-24819248

RESUMEN

The N-terminus of the B-chain of insulin may adopt two alternative conformations designated as the T- and R-states. Despite the recent structural insight into insulin-insulin receptor (IR) complexes, the physiological relevance of the T/R transition is still unclear. Hence, this study focused on the rational design, synthesis, and characterization of human insulin analogues structurally locked in expected R- or T-states. Sites B3, B5, and B8, capable of affecting the conformation of the N-terminus of the B-chain, were subjects of rational substitutions with amino acids with specific allowed and disallowed dihedral φ and ψ main-chain angles. α-Aminoisobutyric acid was systematically incorporated into positions B3, B5, and B8 for stabilization of the R-state, and N-methylalanine and d-proline amino acids were introduced at position B8 for stabilization of the T-state. IR affinities of the analogues were compared and correlated with their T/R transition ability and analyzed against their crystal and nuclear magnetic resonance structures. Our data revealed that (i) the T-like state is indeed important for the folding efficiency of (pro)insulin, (ii) the R-state is most probably incompatible with an active form of insulin, (iii) the R-state cannot be induced or stabilized by a single substitution at a specific site, and (iv) the B1-B8 segment is capable of folding into a variety of low-affinity T-like states. Therefore, we conclude that the active conformation of the N-terminus of the B-chain must be different from the "classical" T-state and that a substantial flexibility of the B1-B8 segment, where GlyB8 plays a key role, is a crucial prerequisite for an efficient insulin-IR interaction.


Asunto(s)
Insulina/análogos & derivados , Insulina/química , Ácidos Aminoisobutíricos/química , Dicroismo Circular , Cristalografía por Rayos X , Humanos , Modelos Moleculares , Estructura Molecular , Resonancia Magnética Nuclear Biomolecular
17.
J Biol Chem ; 288(22): 15800-12, 2013 May 31.
Artículo en Inglés | MEDLINE | ID: mdl-23589369

RESUMEN

Corynebacterium glutamicum is an important industrial bacterium as well as a model organism for the order Corynebacteriales, whose citric acid cycle occupies a central position in energy and precursor supply. Expression of aconitase, which isomerizes citrate into isocitrate, is controlled by several transcriptional regulators, including the dimeric aconitase repressor AcnR, assigned by sequence identity to the TetR family. We report the structures of AcnR in two crystal forms together with ligand binding experiments and in vivo studies. First, there is a citrate-Mg(2+) moiety bound in both forms, not in the canonical TetR ligand binding site but rather in a second pocket more distant from the DNA binding domain. Second, the citrate-Mg(2+) binds with a KD of 6 mM, within the range of physiological significance. Third, citrate-Mg(2+) lowers the affinity of AcnR for its target DNA in vitro. Fourth, analyses of several AcnR point mutations provide evidence for the possible involvement of the corresponding residues in ligand binding, DNA binding, and signal transfer. AcnR derivatives defective in citrate-Mg(2+) binding severely inhibit growth of C. glutamicum on citrate. Finally, the structures do have a pocket corresponding to the canonical tetracycline site, and although we have not identified a ligand that binds there, comparison of the two crystal forms suggests differences in the region of the canonical pocket that may indicate a biological significance.


Asunto(s)
Proteínas Bacterianas/química , Ácido Cítrico/química , Corynebacterium glutamicum/química , Magnesio/química , Factores de Transcripción/química , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Sitios de Unión , Ácido Cítrico/metabolismo , Corynebacterium glutamicum/genética , Corynebacterium glutamicum/metabolismo , Cristalografía por Rayos X , ADN Bacteriano/química , ADN Bacteriano/genética , ADN Bacteriano/metabolismo , Magnesio/metabolismo , Unión Proteica , Factores de Transcripción/genética , Factores de Transcripción/metabolismo
18.
J Biol Chem ; 288(15): 10230-40, 2013 Apr 12.
Artículo en Inglés | MEDLINE | ID: mdl-23447530

RESUMEN

Despite the recent first structural insight into the insulin-insulin receptor complex, the role of the C terminus of the B-chain of insulin in this assembly remains unresolved. Previous studies have suggested that this part of insulin must rearrange to reveal amino acids crucial for interaction with the receptor. The role of the invariant Phe(B24), one of the key residues of the hormone, in this process remains unclear. For example, the B24 site functionally tolerates substitutions to D-amino acids but not to L-amino acids. Here, we prepared and characterized a series of B24-modified insulin analogues, also determining the structures of [D-HisB24]-insulin and [HisB24]-insulin. The inactive [HisB24]-insulin molecule is remarkably rigid due to a tight accommodation of the L-His side chain in the B24 binding pocket that results in the stronger tethering of B25-B28 residues to the protein core. In contrast, the highly active [D-HisB24]-insulin is more flexible, and the reverse chirality of the B24C(α) atom swayed the D-His(B24) side chain into the solvent. Furthermore, the pocket vacated by Phe(B24) is filled by Phe(B25), which mimics the Phe(B24) side and main chains. The B25→B24 downshift results in a subsequent downshift of Tyr(B26) into the B25 site and the departure of B26-B30 residues away from the insulin core. Our data indicate the importance of the aromatic L-amino acid at the B24 site and the structural invariance/integrity of this position for an effective binding of insulin to its receptor. Moreover, they also suggest limited, B25-B30 only, unfolding of the C terminus of the B-chain upon insulin activation.


Asunto(s)
Insulina/química , Sitios de Unión , Humanos , Insulina/genética , Insulina/metabolismo , Unión Proteica/fisiología , Estructura Secundaria de Proteína , Receptor de Insulina/química , Receptor de Insulina/genética , Receptor de Insulina/metabolismo , Relación Estructura-Actividad
19.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 1): 186-95, 2014 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-24419391

RESUMEN

The mammalian O-GlcNAc hydrolysing enzyme O-GlcNAcase (OGA) is a multi-domain protein with glycoside hydrolase activity in the N-terminus and with a C-terminal domain that has low sequence similarity to known acetyltransferases, prompting speculation, albeit controversial, that the C-terminal domain may function as a histone acetyltransferase (HAT). There are currently scarce data available regarding the structure and function of this C-terminal region. Here, a bacterial homologue of the human OGA C-terminal domain, an acetyltransferase protein (accession No. ZP_05014886) from Streptomyces sviceus (SsAT), was cloned and its crystal structure was solved to high resolution. The structure reveals a conserved protein core that has considerable structural homology to the acetyl-CoA (AcCoA) binding site of GCN5-related acetyltransferases (GNATs). Calorimetric data further confirm that SsAT is indeed able to bind AcCoA in solution with micromolar affinity. Detailed structural analysis provided insight into the binding of AcCoA. An acceptor-binding cavity was identified, indicating that the physiological substrate of SsAT may be a small molecule. Consistent with recently published work, the SsAT structure further questions a HAT function for the human OGA domain.


Asunto(s)
Acetiltransferasas/química , Streptomyces/enzimología , beta-N-Acetilhexosaminidasas/química , Acetilcoenzima A/metabolismo , Acetiltransferasas/metabolismo , Sitios de Unión , Cristalografía por Rayos X , Humanos , Modelos Moleculares , Unión Proteica , Estructura Terciaria de Proteína , Streptomyces/química , beta-N-Acetilhexosaminidasas/metabolismo
20.
Acta Crystallogr D Biol Crystallogr ; 70(Pt 10): 2765-74, 2014 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-25286859

RESUMEN

The structural characterization of the insulin-insulin receptor (IR) interaction still lacks the conformation of the crucial B21-B30 insulin region, which must be different from that in its storage forms to ensure effective receptor binding. Here, it is shown that insulin analogues modified by natural amino acids at the TyrB26 site can represent an active form of this hormone. In particular, [AsnB26]-insulin and [GlyB26]-insulin attain a B26-turn-like conformation that differs from that in all known structures of the native hormone. It also matches the receptor interface, avoiding substantial steric clashes. This indicates that insulin may attain a B26-turn-like conformation upon IR binding. Moreover, there is an unexpected, but significant, binding specificity of the AsnB26 mutant for predominantly the metabolic B isoform of the receptor. As it is correlated with the B26 bend of the B-chain of the hormone, the structures of AsnB26 analogues may provide the first structural insight into the structural origins of differential insulin signalling through insulin receptor A and B isoforms.


Asunto(s)
Insulina/análogos & derivados , Insulina/química , Receptor de Insulina/química , Sustitución de Aminoácidos , Animales , Células Cultivadas , Cristalografía por Rayos X , Fibroblastos/metabolismo , Humanos , Insulina/genética , Insulina/metabolismo , Linfocitos/metabolismo , Masculino , Ratones , Ratones Noqueados , Modelos Moleculares , Mutación , Fenilalanina , Conformación Proteica , Ratas Wistar , Receptor de Insulina/metabolismo
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