<i>Phaser</i>crystallographic software

McCoy, Airlie J.; Grosse‐Kunstleve, Ralf W.; Adams, Paul D.; Winn, Martyn; Storoni, Laurent C.; Read, Randy J.

doi:10.1107/s0021889807021206

Cited by 18,805 publications

(14,999 citation statements)

References 62 publications

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“…The McjD‐ADP‐VO 4 structure was determined by molecular replacement in Phaser (McCoy et al , 2007) using our previously published McjD structure (PDB ID: 4PL0; Choudhury et al , 2014) as search model. 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).…”

Section: Methodsmentioning

confidence: 99%

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%

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

et al. 2017

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“…The datasets were integrated and scaled using the HKL-2000 software [58]. The initial phases were calculated by the molecular replacement method using the software Phaser [59]. The coordinate of the anti-OspA Fab fragment (PDB ID: 1FJ1) was used as a search model.…”

Section: Methodsmentioning

confidence: 99%

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

Handoko¹,

Kaczkowski²,

Hon³

et al. 2018

Epigenetics

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The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed, suggesting that recruitment of BRD2 does not influence global histone H4 hyperacetylation levels. This finding supports a model in which recruitment of BET proteins via histone H4 hyperacetylation is predominant over hyperacetylation of histone H4 by BET protein-associated acetyltransferases. In addition, we found that a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and -independent manner.

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“…Refinement was attempted at higher resolution, but this resulted in significantly higher R‐factors and noisy maps. The Se‐SAD structure was used as a model for molecular replacement with PHASER 61, the output of which was again refined using COOT and REFMAC5. Geometric restraints were relaxed somewhat relative to those recommended by Engh and Huber 62 based on recommendations by Jaskolski et al .…”

Section: Experimental Methodsmentioning

confidence: 99%

The molecular structure of the glycoside hydrolase domain of Cwp19 from Clostridium difficile

et al. 2017

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Clostridium difficile is a burden to healthcare systems around the world, causing tens of thousands of deaths annually. The S‐layer of the bacterium, a layer of protein found of the surface of cells, has received a significant amount of attention over the past two decades as a potential target to combat the growing threat presented by C. difficile infections. The S‐layer contains a wide range of proteins, each of which possesses three cell wall‐binding domains, while many also possess a “functional” region. Here, we present the high resolution structure of the functional region of one such protein, Cwp19 along with preliminary functional characterisation of the predicted glycoside hydrolase. Cwp19 has a TIM barrel fold and appears to possess a high degree of substrate selectivity. The protein also exhibits peptidoglycan hydrolase activity, an order of magnitude slower than that of lysozyme and is the first member of glycoside hydrolase‐like family 10 to be characterised. This research goes some way to understanding the role of Cwp19 in the S‐layer of C. difficile.DatabaseStructural data are available in the PDB under the accession numbers 5OQ2 and 5OQ3.

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Phasercrystallographic software

Cited by 18,805 publications

References 62 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

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states

The molecular structure of the glycoside hydrolase domain of Cwp19 from Clostridium difficile

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