Refinement of severely incomplete structures with maximum likelihood in<i>BUSTER–TNT</i>

Blanc, Eric; Roversi, Pietro; Vonrhein, Clemens; Flensburg, Claus; Lea, Susan M.; Bricogne, G.

doi:10.1107/s0907444904016427

Cited by 684 publications

(615 citation statements)

References 36 publications

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“…Initial refinement to 3.4 Å was carried out in REFMAC5 (Murshudov et al , 1997) and at later stages in Buster (Blanc et al , 2004). The structure was refined with restraints against the high‐resolution structure 4PL0.…”

Section: Methodsmentioning

confidence: 99%

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Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

et al. 2017

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Certain pathogenic bacteria produce and release toxic peptides to ensure either nutrient availability or evasion from the immune system. These peptides are also toxic to the producing bacteria that utilize dedicated ABC transporters to provide self‐immunity. The ABC transporter McjD exports the antibacterial peptide MccJ25 in Escherichia coli. Our previously determined McjD structure provided some mechanistic insights into antibacterial peptide efflux. In this study, we have determined its structure in a novel conformation, apo inward‐occluded and a new nucleotide‐bound state, high‐energy outward‐occluded intermediate state, with a defined ligand binding cavity. Predictive cysteine cross‐linking in E. coli membranes and PELDOR measurements along the transport cycle indicate that McjD does not undergo major conformational changes as previously proposed for multi‐drug ABC exporters. Combined with transport assays and molecular dynamics simulations, we propose a novel mechanism for toxic peptide ABC exporters that only requires the transient opening of the cavity for release of the peptide. We propose that shielding of the cavity ensures that the transporter is available to export the newly synthesized peptides, preventing toxic‐level build‐up.

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Section: Methodsmentioning

confidence: 99%

“…Similar solution could also be obtained using MOLREP in CCP4. Refinement to 4.7 Å was carried out in Buster (Blanc et al , 2004). Good electron density could be observed for both the TMD and NBDs including density for aromatic side chains (Fig 3).…”

Section: Methodsmentioning

confidence: 99%

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

et al. 2017

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“…The resulting electron density maps showed the presence of an octopine in the ligand binding site. Refinement was performed with BUSTER-2.10 (Blanc et al, 2004) with non crystallographic symmetry restraints as all asymmetric units contain two protein molecules. One torsion libration screw-motion group was assigned for each structure.…”

Section: Methodsmentioning

confidence: 99%

Fitness costs restrict niche expansion by generalist niche-constructing pathogens

et al. 2016

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We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant hosts that provide different nutrients: nopaline or octopine, respectively. Previous studies revealed that nopaline-type pathogens may expand their niche to also assimilate octopine in the presence of nopaline, but consequences of this phenomenon on pathogen dynamics in planta were not known. Here, we provided molecular insight into how the transport protein NocT can bind octopine as well as nopaline, contributing to niche expansion. We further showed that despite the ability for niche expansion, nopaline-type pathogens had no competitive advantage over octopine-type pathogens in co-infected plants. We also demonstrated that a single nucleotide polymorphism in the nocR gene was sufficient to allow octopine assimilation by nopaline-type strains even in absence of nopaline. The evolved nocR bacteria had higher fitness than their ancestor in octopine-rich transgenic plants but lower fitness in tumors induced by octopine-type pathogens. Overall, this work elucidates the specialization of A. tumefaciens to particular opine niches and explains why generalists do not always spread despite the advantage associated with broader nutritional niches.

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“…The structure was then refined initially in phenix.refine using experimental phase restraints (39,40). Later, the structures were refined with BUSTER, version 2.10.0 (41)(42)(43), allowing for the inclusion of hydrogen atoms during refinement. The quality of the model continuously improved as checked with MolProbity scores (23).…”

Section: Methodsmentioning

confidence: 99%

Crystal structure of the Leishmania major peroxidase–cytochrome c complex

Jasion

Doukov

Pineda

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

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The causative agent of leishmaniasis is the protozoan parasite Leishmania major . Part of the host protective mechanism is the production of reactive oxygen species including hydrogen peroxide. In response, L. major produces a peroxidase, L. major peroxidase (LmP), that helps to protect the parasite from oxidative stress. LmP is a heme peroxidase that catalyzes the peroxidation of mitochondrial cytochrome c . We have determined the crystal structure of LmP in a complex with its substrate, L. major cytochrome c (LmCytc) to 1.84 Å, and compared the structure to its close homolog, the yeast cytochrome c peroxidase–cytochrome c complex. The binding interface between LmP and LmCytc has one strong and one weak ionic interaction that the yeast system lacks. The differences between the steady-state kinetics correlate well with the Lm redox pair being more dependent on ionic interactions, whereas the yeast redox pair depends more on nonpolar interactions. Mutagenesis studies confirm that the ion pairs at the intermolecular interface are important to both k cat and K M . Despite these differences, the electron transfer path, with respect to the distance between hemes, along the polypeptide chain is exactly the same in both redox systems. A potentially important difference, however, is the side chains involved. LmP has more polar groups (Asp and His) along the pathway compared with the nonpolar groups (Leu and Ala) in the yeast system, and as a result, the electrostatic environment along the presumed electron transfer path is substantially different.

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Refinement of severely incomplete structures with maximum likelihood inBUSTER–TNT

Cited by 684 publications

References 36 publications

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

Structural basis for antibacterial peptide self‐immunity by the bacterial ABC transporter McjD

Fitness costs restrict niche expansion by generalist niche-constructing pathogens

Crystal structure of the Leishmania major peroxidase–cytochrome c complex

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