Relevant bibliographies by topics / Periplasmic binding protein (PBP)

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Academic literature on the topic 'Periplasmic binding protein (PBP)'

Author: Grafiati
Published: 4 June 2021
Last updated: 10 February 2022

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Journal articles on the topic "Periplasmic binding protein (PBP)"

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WANG, Chia-Chang, Derk E. SCHULTZ, and Robert A. NICHOLAS. "Localization of a putative second membrane association site in penicillin-binding protein 1B of Escherichia coli." Biochemical Journal 316, no. 1 (May 15, 1996): 149–56. http://dx.doi.org/10.1042/bj3160149.

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We have shown previously that the periplasmic domain of penicillin-binding protein 1B (PBP 1Bper; residues 90–844) from Escherichia coli is insoluble in the absence of detergents, and can be reconstituted into liposomes [Nicholas, Lamson and Schultz (1993) J. Biol. Chem. 268, 5632–5641]. These data suggested that native PBP 1B contains a membrane association site in addition to its N-terminal transmembrane anchor. We have studied the membrane topology of PBP 1B in greater detail by assessing detergent binding and solubility in the absence of detergents for PBP 1Bper and a set of proteolytic fragments of PBP 1B. PBP 1Bper was shown by three independent methods to bind to detergent micelles, which strongly suggests that the periplasmic domain interacts with the hydrophobic milieu of membrane bilayers. Digestion with high weight ratios of thrombin of purified PBP 1B containing an engineered thrombin cleavage site on the periplasmic side of the transmembrane anchor generated four fragments in addition to PBP 1Bper that varied in size from 71 to 48 kDa. In contrast to PBP 1Bper, all fragments of 67 kDa and smaller were eluted from a gel-filtration column in the absence of detergents and did not bind to detergent micelles. The N-terminal sequences of the four fragments were determined, allowing the cleavage sites to be located in the primary sequence of PBP 1B. These data localize the membrane association site of PBP 1B to a region comprising the first 163 amino acids of the periplasmic domain, which falls within the putative transglycosylase domain. Lipid modification does not appear to be the mechanism by which PBP 1Bper associates with membranes.
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Nakamura, Nozomi, Yoichi Naoe, Akihiro Doi, Yoshitsugu Shiro, and Hiroshi Sugimoto. "Conformational change of periplasmic heme-binding protein in ABC transporter." Acta Crystallographica Section A Foundations and Advances 70, a1 (August 5, 2014): C1496. http://dx.doi.org/10.1107/s2053273314085039.

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Iron is one of the essential elements for all living organisms. Pathogenic bacteria acquire heme from the host proteins as an iron source. Gram-negative opportunistic pathogen, Burkholderia cenocepacia have ATP-binding cassette (ABC) transporter BhuUV-T complex to permeate heme through inner membrane. BhuT, periplasmic binding protein (PBP), bind and deliver heme(s) to inner membrane transporter BhuUV complex. BhuUV is 2:2 complex of the transmembrane permease subunit and cytoplasmic ATP-binding subunit which couple ATP hydrolysis to solute translocation. The molecular level mechanism of heme recognition and dissociation by PBP and heme transport by transporter complex are not fully understood. Here we describe the crystal structures of the heme-free and two types of heme-bound state of BhuT. These crystals were obtained in different crystallization conditions. Crystals diffracted to high resolution at SPring-8. BhuT is composed of two globular domains linked by a long a-helix. The transport ligand heme is bound between the two domains. A detailed structural comparison of the conformation of the domain and residues involved in the heme binding will be presented.
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Pegos, Vanessa R., Louis Hey, Jacob LaMirande, Rachel Pfeffer, Rosalie Lipsh, Moshe Amitay, Daniel Gonzalez, and Mikael Elias. "Phosphate-binding protein fromPolaromonasJS666: purification, characterization, crystallization and sulfur SAD phasing." Acta Crystallographica Section F Structural Biology Communications 73, no. 6 (May 25, 2017): 342–46. http://dx.doi.org/10.1107/s2053230x17007373.

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Phosphate-binding proteins (PBPs) are key proteins that belong to the bacterial ABC-type phosphate transporters. PBPs are periplasmic (or membrane-anchored) proteins that capture phosphate anions from the environment and release them to the transmembrane transporter. Recent work has suggested that PBPs have evolved for high affinity as well as high selectivity. In particular, a short, unique hydrogen bond between the phosphate anion and an aspartate residue has been shown to be critical for selectivity, yet is not strictly conserved in PBPs. Here, the PBP fromPolaromonasJS666 is focused on. Interestingly, this PBP is predicted to harbor different phosphate-binding residues to currently known PBPs. Here, it is shown that the PBP fromPolaromonasJS666 is capable of binding phosphate, with a maximal binding activity at pH 8. Its structure is expected to reveal its binding-cleft configuration as well as its phosphate-binding mode. Here, the expression, purification, characterization, crystallization and X-ray diffraction data collection to 1.35 Å resolution of the PBP fromPolaromonasJS666 are reported.
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Brambilla, Luciano, Jorgelina Morán-Barrio, and Alejandro M. Viale. "Low-Molecular-Mass Penicillin Binding Protein 6b (DacD) Is Required for Efficient GOB-18 Metallo-β-Lactamase Biogenesis in Salmonella enterica and Escherichia coli." Antimicrobial Agents and Chemotherapy 58, no. 1 (October 21, 2013): 205–11. http://dx.doi.org/10.1128/aac.01224-13.

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ABSTRACTMetallo-β-lactamases (MBLs) are Zn2+-containing secretory enzymes of clinical relevance, whose final folding and metal ion assembly steps in Gram-negative bacteria occur after secretion of the apo form to the periplasmic space. In the search of periplasmic factors assisting MBL biogenesis, we found thatdacDnull (ΔdacD) mutants ofSalmonella entericaandEscherichia coliexpressing the pre-GOB-18 MBL gene from plasmids showed significantly reduced resistance to cefotaxime and concomitant lower accumulation of GOB-18 in the periplasm. This reduced accumulation of GOB-18 resulted from increased accessibility to proteolytic attack in the periplasm, suggesting that the lack of DacD negatively affects the stability of secreted apo MBL forms. Moreover, ΔdacDmutants ofS. entericaandE. colishowed an altered ability to develop biofilm growth. DacD is a widely distributed low-molecular-mass (LMM) penicillin binding protein (PBP6b) endowed with lowdd-carboxypeptidase activity whose functions are still obscure. Our results indicate roles for DacD in assisting biogenesis of particular secretory macromolecules in Gram-negative bacteria and represent to our knowledge the first reported phenotypes for bacterial mutants lacking this LMM PBP.
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de Sousa Borges, Anabela, Jeanine de Keyzer, Arnold J. M. Driessen, and Dirk-Jan Scheffers. "The Escherichia coli Membrane Protein Insertase YidC Assists in the Biogenesis of Penicillin Binding Proteins." Journal of Bacteriology 197, no. 8 (February 9, 2015): 1444–50. http://dx.doi.org/10.1128/jb.02556-14.

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ABSTRACTMembrane proteins need to be properly inserted and folded in the membrane in order to perform a range of activities that are essential for the survival of bacteria. The Sec translocon and the YidC insertase are responsible for the insertion of the majority of proteins into the cytoplasmic membrane. YidC can act in combination with the Sec translocon in the insertion and folding of membrane proteins. However, YidC also functions as an insertase independently of the Sec translocon for so-called YidC-only substrates. In addition, YidC can act as a foldase and promote the proper assembly of membrane protein complexes. Here, we investigate the effect ofEscherichia coliYidC depletion on the assembly of penicillin binding proteins (PBPs), which are involved in cell wall synthesis. YidC depletion does not affect the total amount of the specific cell division PBP3 (FtsI) in the membrane, but the amount of active PBP3, as assessed by substrate binding, is reduced 2-fold. A similar reduction in the amount of active PBP2 was observed, while the levels of active PBP1A/1B and PBP5 were essentially similar. PBP1B and PBP3 disappeared from higher-Mwbands upon YidC depletion, indicating that YidC might play a role in PBP complex formation. Taken together, our results suggest that the foldase activity of YidC can extend to the periplasmic domains of membrane proteins.IMPORTANCEThis study addresses the role of the membrane protein insertase YidC in the biogenesis of penicillin binding proteins (PBPs). PBPs are proteins containing one transmembrane segment and a large periplasmic or extracellular domain, which are involved in peptidoglycan synthesis. We observe that in the absence of YidC, two critical PBPs are not correctly folded even though the total amount of protein in the membrane is not affected. Our findings extend the function of YidC as a foldase for membrane protein (complexes) to periplasmic domains of membrane proteins.
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MAHAPATRA, Sebabrata, Sanjib BHAKTA, Jasimuddin AHAMED, and Joyoti BASU. "Characterization of derivatives of the high-molecular-mass penicillin-binding protein (PBP) 1 of Mycobacterium leprae." Biochemical Journal 350, no. 1 (August 9, 2000): 75–80. http://dx.doi.org/10.1042/bj3500075.

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Mycobacterium leprae has two high-molecular-mass multimodular penicillin-binding proteins (PBPs) of class A, termed PBP1 and PBP1* [Lepage, Dubois, Ghosh, Joris, Mahapatra, Kundu, Basu, Chakrabarti, Cole, Nguyen-Disteche and Ghuysen (1997) J. Bacteriol. 179, 4627–4630]. PBP1-Xaa–β-lactamase fusions generated periplasmic β-lactamase activity when Xaa (the amino acid of PBP1 at the fusion junction) was residue 314, 363, 407, 450 or 480. Truncation of the N-terminal part of the protein up to residue Leu-147 generated a penicillin-binding polypeptide which could still associate with the plasma membrane, whereas [∆M1–R314]PBP1 (PBP1 lacking residues Met-1 to Arg-314) failed to associate with the membrane, suggesting that the region between residues Leu-147 and Arg-314 harbours an additional plasma membrane association site for PBP1. Truncation of the C-terminus up to 42 residues downstream of the KTG (Lys-Thr-Gly) motif also generated a polypeptide that retained penicillin-binding activity. [∆M1–R314]PBP1 could be extracted from inclusion bodies and refolded under appropriate conditions to give a form capable of binding penicillin with the same efficiency as full-length PBP1. This is, to the best of our knowledge, the first report of a soluble derivative of a penicillin-resistant high-molecular-mass PBP of class A that is capable of binding penicillin. A chimaeric PBP in which the penicillin-binding (PB) module of PBP1 was fused at its N-terminal end with the non-penicillin-binding (n-PB) module of PBP1* retained pencillin-binding activity similar to that of PBP1, corroborating the finding that the n-PB module of PBP1 is dispensable for its penicillin-binding activity.
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BHAKTA, Sanjib, and Joyoti BASU. "Overexpression, purification and biochemical characterization of a class A high-molecular-mass penicillin-binding protein (PBP), PBP1∗ and its soluble derivative from Mycobacterium tuberculosis." Biochemical Journal 361, no. 3 (January 25, 2002): 635–39. http://dx.doi.org/10.1042/bj3610635.

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The product of the gene ponA present in cosmid MTCY21D4, one of the collection of clones representing the genome of Mycobacteriumtuberculosis, has been named penicillin-binding protein 1∗ (PBP1∗), by analogy to the previously characterized PBP1∗ of M. leprae. This gene has been overexpressed in Escherichia coli. His6-tagged PBP1∗ localizes to the membranes of induced E. coli cells. Its susceptibility to degradation upon proteinase K digestion of spheroplasts from E. coli expressing the protein supports the view that the majority of the protein translocates to the periplasmic side of the membrane. Recombinant PBP1∗ binds benzylpenicillin and several other β-lactams, notably cefotaxime, with high affinity. Truncation of the N-terminal 64 amino acid residues results in an expressed protein present exclusively in inclusion bodies and unable to associate with the membrane. The C-terminal module encompassing amino acids 272–663 can be extracted from inclusion bodies under denaturing conditions using guanidine/HCl and refolded to give a protein fully competent in penicillin-binding. Deletion of Gly95—Gln143 results in the expression of a protein, which is localized in the cytosol. The soluble derivative of PBP1∗ binds benzylpenicillin with the same efficiency as the full-length protein. This is the first report of a soluble derivative of a class A high-molecular-mass PBP.
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Krewulak, Karla D., and Hans J. Vogel. "TonB or not TonB: is that the question?This paper is one of a selection of papers published in a Special Issue entitled CSBMCB 53rd Annual Meeting — Membrane Proteins in Health and Disease, and has undergone the Journal’s usual peer review process." Biochemistry and Cell Biology 89, no. 2 (April 2011): 87–97. http://dx.doi.org/10.1139/o10-141.

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Bacteria are able to survive in low-iron environments by sequestering this metal ion from iron-containing proteins and other biomolecules such as transferrin, lactoferrin, heme, hemoglobin, or other heme-containing proteins. In addition, many bacteria secrete specific low molecular weight iron chelators termed siderophores. These iron sources are transported into the Gram-negative bacterial cell through an outer membrane receptor, a periplasmic binding protein (PBP), and an inner membrane ATP-binding cassette (ABC) transporter. In different strains the outer membrane receptors can bind and transport ferric siderophores, heme, or Fe3+ as well as vitamin B12, nickel complexes, and carbohydrates. The energy that is required for the active transport of these substrates through the outer membrane receptor is provided by the TonB/ExbB/ExbD complex, which is located in the cytoplasmic membrane. In this minireview, we will briefly examine the three-dimensional structure of TonB and the current models for the mechanism of TonB-dependent energy transduction. Additionally, the role of TonB in colicin transport will be discussed.
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Keegan, Ronan, David G. Waterman, David J. Hopper, Leighton Coates, Graham Taylor, Jingxu Guo, Alun R. Coker, Peter T. Erskine, Steve P. Wood, and Jonathan B. Cooper. "The 1.1 Å resolution structure of a periplasmic phosphate-binding protein fromStenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank." Acta Crystallographica Section D Structural Biology 72, no. 8 (July 27, 2016): 933–43. http://dx.doi.org/10.1107/s2059798316010433.

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During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) fromAlcaligenessp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this new structure as the search model did not give a convincing solution with the original atomic resolution data set. Hence, it was considered that these crystals might have arisen from a protein impurity, although molecular replacement using the structures of common crystallization contaminants as search models again failed. A script to perform molecular replacement usingMOLREPin which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate-binding proteins as scoring highly in theMOLREPpeak lists. Calculation of an electron-density map at 1.1 Å resolution based on the solution obtained with PDB entry 2q9t allowed most of the amino acids to be identified visually and built into the model. ABLASTsearch then indicated that the molecule was most probably a phosphate-binding protein fromStenotrophomonas maltophilia(UniProt ID B4SL31; gene ID Smal_2208), and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked to the virulence of antibiotic-resistant strains of pathogenic bacteria and with biofilm formation. The structure of theS. maltophiliaprotein has been refined to anRfactor of 10.15% and anRfreeof 12.46% at 1.1 Å resolution. The molecule adopts the type II periplasmic binding protein (PBP) fold with a number of extensively elaborated loop regions. A fully dehydrated phosphate anion is bound tightly between the two domains of the protein and interacts with conserved residues and a number of helix dipoles.
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Miller, Kurt W., Robin Schamber, Yanling Chen, and Bibek Ray. "Production of Active Chimeric Pediocin AcH inEscherichia coli in the Absence of Processing and Secretion Genes from the Pediococcus pap Operon." Applied and Environmental Microbiology 64, no. 1 (January 1, 1998): 14–20. http://dx.doi.org/10.1128/aem.64.1.14-20.1998.

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ABSTRACT Minimum requirements have been determined for synthesis and secretion of the Pediococcus antimicrobial peptide, pediocin AcH, in Escherichia coli. The functional mature domain of pediocin AcH (Lys+1 to Cys+44) is targeted into the E. coli sec machinery and secreted to the periplasm in active form when fused in frame to the COOH terminus of the secretory protein maltose-binding protein (MBP). The PapC-PapD specialized secretion machinery is not required for secretion of the MBP-pediocin AcH chimeric protein, indicating that inPediococcus, PapC and PapD probably are required for recognition and processing of the leader peptide rather than for translocation of the mature pediocin AcH domain across the cytoplasmic membrane. The chimeric protein displays bactericidal activity, suggesting that the NH2 terminus of pediocin AcH does not span the phospholipid bilayer in the membrane-interactive form of the molecule. However, the conserved Lys+1-Tyr-Tyr-Gly-Asn-Gly-Val+7-sequence at the NH2 terminus is important because deletion of this sequence abolishes activity. The secreted chimeric protein is released into the culture medium when expressed in a periplasmic leaky E. coli host. The MBP fusion-periplasmic leaky expression system should be generally advantageous for production and screening of the activity of bioactive peptides.
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Dissertations / Theses on the topic "Periplasmic binding protein (PBP)"

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Vigouroux, Armelle. "Structures et spécificités de protéines périplasmiques de liaison (PBP) des mannityl-opines et des sucres de la famille du raffinose (RFO) chez Agrobacterium tumefaciens." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS541.

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La bactérie Agrobacterium tumefaciens établit une relation à long terme avec les plantes. Elle peut avoir deux modes de vie : (1) pathogène lorsqu’elle possède le plasmide de virulence Ti (Tumor inducing) provoquant la maladie de la galle du collet caractérisée par la formation de tumeur chez la plante, (2) non pathogène vivant dans la rhizosphère. Dans ces deux modes de vie, Agrobacterium utilise les PBP (protéines périplasmiques de liaision) associées à des transporteurs ABC pour importer des molécules issues de plante servant de nutriments. La PBP sélectionne et fixe le ligand qu’elle apporte au transporteur ABC, qui permet son passage dans le cytoplasme grâce à l’hydrolyse de deux molécules d’ATP. La spécificité du transporteur entier dépend de la PBP. Les molécules transportées et dégradées par la bactérie apparaissent comme un avantage trophique pour la colonisation de l’environnement.Lorsqu’A. tumefaciens est pathogène, la bactérie transfère une partie de son plasmide Ti dans le génome des cellules végétales, induisant la production et sécrétion par la plante de composés spécifiques pour la bactérie, appelés opines. Une vingtaine d’opines sont connues à ce jour, et chacune d’elles peut être métabolisée par des souches d’A. tumefaciens. La souche B6 possède un pTi de type octopine, qui porte les gènes de métabolisme de la famille des mannityl-opines, composée de l’acide agropinique, l’agropine, l’acide mannopinique et la mannopine. D’après des études génétiques chez des souches de type octopine, les systèmes PBP-transporteur ABC associés sont respectivement AgaABCD, AgtABCD, MoaABCD et MotABCD.Dans la rhizosphère, les graines en germination influencent la composition de la rhizosphère et favorisent la croissance de microorganismes en libérant des molécules telles que les sucres de la famille du raffinose (RFO, Raffinose Family of Oligosaccharides). Des analyses in silico d’Agrobacterium fabrum C58 indiquent que la souche possèderait un opéron que nous avons appelé mel, proche de l’opéron agp chez Ensifer meliloti 1021 décrit comme responsable du transport et de la dégradation des RFO qui semble influer sur la survie de la bactérie dans la rhizosphère. Nous avons fait l’hypothèse que la PBP MelB de l’opéron mel chez A. fabrum C58 est responsable du transport des RFO.Mon travail de thèse a permis de finaliser la caractérisation structurale et biochimique des transporteurs des mannityl-opines et a permis l’identification et la caractérisation de MelB comme responsable de l’import des RFO et du galactinol (précurseur des RFO). Le transport et la dégradation des molécules transportées par ces PBP sont importants pour la colonisation de leur environnement
Agrobacterium tumefaciens bacterium establishes a long-term relationship with plants. It can have two lifestyles: (1) pathogenic when it harbors the virulence plasmid Ti (Tumor inducing) causing the crown gall disease characterized by tumor formation in plant, (2) non-pathogenic living in the rhizosphere. In these two lifestyles, Agrobacterium uses PBP (periplasmic binding proteins) associated with ABC transporters to import molecules from plants as nutrients. PBP selects and binds the ligand that it brings to the ABC transporter, which allows its passage into the cytoplasm by the hydrolysis of two ATP molecules. The specificity of the entire transporter depends on PBP. The molecules transported and degraded by the bacteria appear as a trophic advantage for the colonization of the environment.When A. tumefaciens is pathogenic, the bacterium transfers part of its Ti plasmid into the genome of plant cells, inducing the production and secretion by the plant of specific compounds for the bacterium, called opines. Twenty opines are known to date, and each of them can be metabolized by A. tumefaciens strains. The strain B6 possesses an octopine-type pTi, which harbors metabolism genes of the mannityl-opines family, composed of agropinic acid, agropine, mannopinic acid and mannopine. According to genetic studies in octopine type strains, the associated PBP-transporter ABC systems are AgaABCD, AgtABCD, MoaABCD and MotABCD, respectively.In the rhizosphere, germinating seeds influence the composition of the rhizosphere and promote the growth of microorganisms by releasing molecules such as Raffinose Family of Oligosaccharides (RFO). In silico analyzes of Agrobacterium fabrum C58 indicate that the strain possesses an operon we called mel, similar to the agp operon in Ensifer meliloti 1021 described as responsible for the transport and degradation of RFOs that appears to influence the survival of the bacterium in the rhizosphere. We hypothesized that the PBP MelB of the mel operon in A. fabrum C58 is responsible for the transport of the RFOs.My thesis work allowed to finalize the structural and biochemical characterization of mannityl-opines transporters and allowed the identification and characterization of MelB as responsible for the import of RFO and galactinol (precursor of the RFO). The transport and degradation of the molecules transported by these PBPs are important for the colonization of their environment
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Forward, Jason Andrew. "Mechanism of a novel class periplasmic binding protein dependent solute transport system." Thesis, University of Sheffield, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.389733.

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Robinson, Renee. "A heme periplasmic-binding protein hHBP mediates heme transport in Haemophilus ducreyi." Thesis, University of Ottawa (Canada), 2010. http://hdl.handle.net/10393/28801.

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Haemophilus ducreyi, a Gram-negative and heme-dependent bacterium, is the causative agent of chancroid, a genital ulcer sexually transmitted infection. Although the precise molecular mechanism of heme acquisition in H. ducreyi is unclear, heme uptake likely proceeds via a receptor mediated process. The initial event involves binding to either of two outer membrane receptors, TdhA and HgbA. Once heme is deposited into the periplasmic space, a heme permease is postulated to transport heme across the periplasmic space to the inner membrane. In prior experiments, using protein expression profiling of the H. ducreyi periplasmic proteome, we identified a periplasmic-binding protein hHBP that we propose is a component of a heme trafficking operon. Biochemical and genetic approaches were used to functionally characterize hHBP. First, purified hHBP was incubated with increasing concentrations of heme and the mixtures were resolved by non-denaturing polyacylamide gel electrophoresis. Separated proteins were transferred onto PVDF membranes and heme-protein complexes were detected by enhanced chemiluminescence (ECL). Second, the hhbp gene was cloned in the E. coli recombinant mutant E. coli FB827 dppA::Km mppA::Cm (pAM238-HasR) which expresses the Serratia marcescens HasR heme receptor allowing heme translocaton into the periplasm, but denies heme entry into the cytoplasm because of the presence of the double mutation (dppA::Km mppA::Cm) resulting in a mutant lacking the two periplasmic proteins DppA and MppA. We found that heme binding to hHBP was saturable as determined by ECL. Genetic complementation in trans with hhbp repaired the growth defect of the mutant E. coli for heme utilization as an iron source. The growth restoration was comparable to that seen with the E. coli mutant complemented with the intact Dpp permease. Additionally, growth of the mutant was not rescued with the empty plasmid vector. We concluded that H. ducreyi hHBP functionally binds heme. Complementation of the E. coli mutant for heme competency supports the proposal that hHBP participates in the transit of heme in H. ducreyi.
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St, Denis Melissa. "Identification and characterization of a heme-dedicated periplasmic binding protein in Haemophilus ducreyi." Thesis, University of Ottawa (Canada), 2007. http://hdl.handle.net/10393/27487.

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In Haemophilus ducreyi, heme uptake likely proceeds via a receptor-mediated process. The initial event involves binding to either of two outer membrane receptors, TdhA and HgbA. Once heme is deposited into the periplasmic space, we hypothesize that a heme-dedicated periplasmic binding protein (hHBP) is responsible for transporting heme across the periplasmic space to the inner membrane. To identify the hHBP, periplasmic extracts were generated from H. ducreyi 35000 grown under high and low heme conditions and subjected to proteome mapping. Peptide sequences of upregulated proteins grown under heme-restrictive conditions were determined by mass spectroscopy. A candidate hHBP was identified as a periplasmic binding protein homologous to YfeA of Yersinia pestis. The gene encoding this protein appears to be in a typical ABC transporter operon. Under iron-limiting conditions, no upregulation of the hHBP expression was observed; however, the purified hHBP was shown to specifically bind heme in a concentration-dependent manner.
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Magnusson, Ulrika. "Structural Studies of Binding Proteins: Investigations of Flexibility, Specificity and Stability." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3640.

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Björkman, A. Joakim. "Structure-function studies of the periplasmic ribose-binding protein, a receptor in bacterial chemotaxis and transport /." Uppsala : Swedish Univ. of Agricultural Sciences (Sveriges lantbruksuniv.), 1998. http://epsilon.slu.se/avh/1998/91-576-5545-6.gif.

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Wei, Yuping. "Characterization of two Bacillus subtilis penicillin-binding protein-coding genes, ykuA (pbpH) and yrrR (pbpI)." Thesis, Virginia Tech, 2002. http://hdl.handle.net/10919/34900.

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Penicillin-binding proteins (PBPs) are required in the synthesis of the cell wall of bacteria. In Bacillus subtilis, PBPs play important roles in the life cycle, including both vegetative growth and sporulation, and contribute to the formation of the different structures of vegetative cell wall and spore cortex. The B. subtilis genome sequencing project revealed there were two uncharacterized genes, ykuA and yrrR, with extensive sequence similarity to class B PBPs. These two genes are renamed and referred to henceforth as pbpH and pbpI, respectively.

A sequence alignment of the predicted product of pbpH against the microbial protein database demonstrated that the most similar protein in B. subtilis is PBP2A and in E. coli is PBP2. This suggested that PbpH belongs to a group of the genes required for maintaining the rod shape of the cell. Study of a pbpH-lacZ fusion showed that pbpH was expressed weakly during vegetative growth and the expression reached the highest level at the transition from exponential phase to stationary phase. The combination of a pbpA deletion and the pbpH deletion was lethal and double mutant strains lacking pbpH and pbpC or pbpI (also named yrrR) were viable. The viable mutants were indistinguishable from the wild-type except that the vegetative PG of the pbpC pbpH strain had a slightly slightly lower amount of disaccharide tetrapeptide with 1 amidation and higher amount of disaccharide tripeptide tetrapeptide with 2 amidations when compared to others strains. This suggests that PbpC (PBP3) is involved in vegetative PG synthesis but only affects the PG structure with a very low efficiency.

A pbpA pbpH double mutant containing a xylose-regulated pbpH gene inserted into the chromosome at the amyE locus was constructed. Depletion of PbpH resulted in an arrest in cell growth and a dramatic morphological change in both vegetative cells and outgrowing spores. Vegetative cells lacking pbpA and pbpH expression swelled and cell elongation was arrested, leading to the formation of pleiomorphic spherical cells and eventual lysis. In these cells, cell septations were randomly localized, cell walls and septa were thicker than those seen in wild type cells, and the average cell width and volume were larger than those of cells expressing pbpA or pbpH. The vegetative PG had an increased abundance of one unidentified muropeptide. Spores produced by the pbpA pbpH double mutant were able to initiate germination but the transition of the oval-shaped spores to rod-shape cells was blocked. The outgrowing cells were spherical, gradually enlarged, and eventually lysed. Outgrowth of these spores in the presence of xylose led to the formation of helical cells. Thus, PbpH is apparently required for maintenance of cell shape, specifically for cell elongation. PbpH and PBP2a play a redundant role homologous to that of PBP2 in E. coli.

A sequence alignment of the predicted product of pbpI against the microbial protein database demonstrated that the most similar protein in B. subtilis is SpoVD and in E. coli is PBP3. This suggested that PbpI belongs to the group of the genes required for synthesis of the spore or septum PG. PbpI was identified using radio-labeled penicillin and found to run underneath PBP4 on SDS-PAGE. PbpI is therefore renamed PBP4b. Study of a pbpI-lacZ fusion showed that pbpI was expressed predominantly during early sporulation. A putative sigma F recognition site is present in the region upstream of pbpI and studies using mutant strains lacking sporulation-specific sigma factors demonstrated that the expression of pbpI is mainly dependent on sigma factor F. A pbpI single mutant, a pbpI pbpG double mutant, and a pbpI pbpF double mutant were indistinguishable from the wild-type. The sporulation defect of a pbpI pbpF pbpG triple mutant was indistinguishable from that of a pbpF pbpG double mutant. Structure parameters of the forespore PG in a pbpI spoVD strain are similar to that of a spoVD strain. These results indicate that PBP4b plays a unknown redundant role.


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Dean, Amanda Marie. "Requirements for Compartmentalization of Penicillin-Binding Proteins during Sporulation in Bacillus subtilis." Thesis, Virginia Tech, 2002. http://hdl.handle.net/10919/36489.

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Penicillin-binding proteins (PBP's) are membrane-associated enzymes involved in the polymerization of peptidoglycan. PBP's are divided into three classes based upon their molecular weights and functional domains. Gene expression is regulated in the two differentiated cells in Bacillus subtilis, the mother cell and the forespore, by coordinated expression of different sigma factors that recognize specific promoters in each compartment. The functional and compartmental specificity of individual penicillin-binding proteins from the different classes of PBP's were examined during sporulation in B. subtilis. Analyses of three class A high molecular weight PBP's indicated that pbpF and pbpG must be expressed in the forespore to carry out their specific role during spore peptidoglycan synthesis. Expressing pbpD in either the forespore or the mother cell could not complement for the loss of pbpF and pbpG, suggesting that there must be additional sequence information in PBP2c and PBP2d that allows them to carry out their specific role during germ cell wall synthesis. Analyses of a low molecular weight PBP, PBP5*, suggested that expressing dacB in either the mother cell or in the forespore could regulate the level of spore peptidoglycan cross-linking to what is typical of wild type spore peptidoglycan.
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9

Loftin, Isabell. "Structural and Biochemical Studies of the Metal Binding Protein CusF and its Role in Escherichia coli Copper Homeostasis." Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/193875.

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Biometals such as copper, cobalt and zinc are essential to life. These transition metals are used as cofactors in many enzymes. Nonetheless, these metals cause deleterious effects if their intracellular concentration exceeds the cells' requirement. Prokaryotic organisms usually employ efflux systems to maintain metals in appropriate intracellular concentrations.The Cus system of Escherichia coli plays a crucial part in the copper homeostasis of the organism. This system is a tetrapartite efflux system, which includes an additional component compared to similar efflux systems. This fourth component is a small periplasmic protein, CusF. CusF is essential for full copper resistance, yet its role within the Cus system has not been characterized. It could potentially serve in the role of a metallochaperone or as a regulator to the Cus system.To gain insight into the molecular mechanism of resistance of this system, I have structurally and biochemically characterized CusF. Using X-ray crystallography I determined the CusF structure. CusF displays a novel fold for a copper binding protein. Through multiple sequence alignment and NMR chemical shift experiments, I proposed a metal binding site in CusF, which I confirmed through determination of the structure of CusF-Ag(I). CusF displays a novel coordination of Ag(I) and Cu(I) through a Met2His motif and a cation-pi interaction between the metal ion and a tryptophan sidechain. Furthermore, I have shown that CusF binds Cu(I) and Ag(I) specifically and tightly.I investigated the role of the tryptophan at the binding site to establish its effect on metal binding and function of CusF. I have shown through competitive binding assays, NMR studies and through collaborative EXAFS studies that the tryptophan plays an essential role in CusF metal handling. The affinity of CusF for Cu(I) is influenced by this residue. Moreover, the tryptophan also caps the binding site such that oxidation of the bound metal as well access to adventitious ligands is prevented. In summary, these findings show that the structure and metal site of CusF are unique and are specifically designed to perform the function of CusF as a metallochaperone to the Cus system.
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Ferreira, Francisco C. "Periplasmic binding protein FhuD of Escherichia coli K-12 : overexpression in Bacillus subtilis, purification, and renaturation of the recombinant FhuD." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape10/PQDD_0005/MQ44166.pdf.

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Books on the topic "Periplasmic binding protein (PBP)"

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Ünligil, Uluğ Mete. Protein structure and evolution: A study of the X-ray crystal structures of rabbit N-acetylglucosaminyltransferase I and haemophilus influenzae periplasmic zinc-binding protein 1. 2002.

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Book chapters on the topic "Periplasmic binding protein (PBP)"

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Quiocho, F. A., N. K. Vyas, J. S. Sack, and M. A. Storey. "Periplasmic Binding Proteins: Structures and New Understanding of Protein-Ligand Interactions." In Crystallography in Molecular Biology, 385–94. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4684-5272-3_35.

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Króliczewski, Jarosław, and Andrzej Szczepaniak. "Localisation of Apocytochrome b 6 Fused to Expressed Periplasmic Maltose-binding Protein in Escherichia coli." In Photosynthesis: Mechanisms and Effects, 1557–60. Dordrecht: Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-011-3953-3_366.

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Garvis, S. G., G. J. Puzon, and M. E. Konkel. "Cloning, Sequencing, and Expression of a Campylobacter Jejuni Periplasmic Binding Protein (P29) Involved in Histidine Transport." In Advances in Experimental Medicine and Biology, 263–64. Boston, MA: Springer US, 1997. http://dx.doi.org/10.1007/978-1-4899-1828-4_42.

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Sagot, B., G. Alloing, D. Hérouart, D. Le Rudulier, and L. Dupont. "Identification of BetX, a Periplasmic Protein Involved in Binding and Uptake of Proline Betaine and Glycine Betaine in Sinorhizobium meliloti." In Biological Nitrogen Fixation: Towards Poverty Alleviation through Sustainable Agriculture, 265. Dordrecht: Springer Netherlands, 2008. http://dx.doi.org/10.1007/978-1-4020-8252-8_101.

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"Prostatic Binding Protein (PBP)." In Encyclopedia of Signaling Molecules, 4200. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-67199-4_103089.

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Hunt, Arthur G., and Jen-Shiang Hong. "[24] Reconstitution of periplasmic binding protein-dependent glutamine transport in vesicles." In Methods in Enzymology, 302–9. Elsevier, 1986. http://dx.doi.org/10.1016/s0076-6879(86)25026-0.

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Brass, Johann M. "[23] Calcium-induced permeabilization of the outer membrane: A method for reconstitution of periplasmic binding protein-dependent transport systems in Escherichia coli and Salmonella typhimurium." In Methods in Enzymology, 289–302. Elsevier, 1986. http://dx.doi.org/10.1016/s0076-6879(86)25025-9.

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