Presenting your structures: the<i>CCP</i>4<i>mg</i>molecular-graphics software

McNicholas, Stuart; Potterton, E. A.; Wilson, K.S.; Noble, M.E.M.

doi:10.1107/s0907444911007281

Cited by 1,199 publications

(945 citation statements)

References 36 publications

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“…Insert: zoom in projection of a putative hemin-binding pocket in dimeric PE. Docking was performed manually using COOT (Emsley et al, 2010;McNicholas et al, 2011;Potterton et al, 2002). The figures were prepared with Pymol and CCP4MG.…”

Section: Discussionmentioning

confidence: 99%

Haemophilus influenzae stores and distributes hemin by using Protein E

Jubair

Singh

Fleury

et al. 2014

International Journal of Medical Microbiology

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Section: Discussionmentioning

confidence: 99%

Haemophilus influenzae stores and distributes hemin by using Protein E

Jubair

Singh

Fleury

et al. 2014

International Journal of Medical Microbiology

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“…The model was based on the chick ACTG2 crystal structure with a protein sequence identical to that of human ACTG2. The Swiss model 22 was used to create 14-mer models of the two protein variants and the CCP4mg software 23 was used for 3D visualization of residue 269 in ACTG2, as well as its relative position to adjacent amino acids.…”

Section: D Modeling Of the Actg2mentioning

confidence: 99%

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution

et al. 2015

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Familial visceral myopathy (FVM) is a rare heritable and heterogeneous condition due to impaired smooth muscle function. We identified a family segregating 11 individuals with a spectrum of visceral symptoms involving the small intestine, colon, biliary tract, urinary tract and uterus. Whole-exome sequencing revealed a novel heterozygous tandem base substitution c.806_807delinsAA (p.(Gly269Glu)) in ACTG2, encoding smooth muscle actin γ-2, in affected family members. Variants in ACTG2 were recently identified in FVM with intestinal pseudo-obstruction as well as with the congenital megacystics-microcolonintestinal hypoperistalsis syndrome. In our family, eight affected members presented with severe complications from the biliary and/or the urinary tracts in addition to gastrointestinal pseudo-obstructions. Furthermore, all affected mothers had a history of assisted deliveries owing to poor progress during labor and weak uterine contractions. The variable involvement of multiple smooth muscle-dependent organs in our family, including the biliary tract and the uterus, add to the phenotypic spectrum associated with ACTG2 missense variants.

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“…Cutinases (EC 3.1.1.74, Pfam family PF01083) are small (20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30) lipolytic enzymes capable of hydrolyzing a wide variety of esters, including triglycerides of varying size. To date, the threedimensional (3D) structure has been reported for three cutinases, from Fusarium solani (FsC), 1 Glomerella cingulata (GcC), 2,3 and Aspergillus oryzae (AoC).…”

Section: Introductionmentioning

confidence: 99%

Thermodynamic and structural investigation of the specific SDS binding of humicola insolens cutinase

et al. 2014

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The interaction of lipolytic enzymes with anionic surfactants is of great interest with respect to industrially produced detergents. Here, we report the interaction of cutinase from the thermophilic fungus Humicola insolens with the anionic surfactant SDS, and show the enzyme specifically binds a single SDS molecule under nondenaturing concentrations. Protein interaction with SDS was investigated by NMR, ITC and molecular dynamics simulations. The NMR resonances of the protein were assigned, with large stretches of the protein molecule not showing any detectable resonances. SDS is shown to specifically interact with the loops surrounding the catalytic triad with medium affinity (K a % 10 5 M 21 ). The mode of binding is closely similar to that seen previously for binding of amphiphilic molecules and substrate analogues to cutinases, and hence SDS acts as a substrate mimic. In addition, the structure of the enzyme has been solved by X-ray crystallography in its apo form and after cocrystallization with diethyl p-nitrophenyl phosphate (DNPP) leading to a complex with monoethylphosphate (MEP) esterified to the catalytically active serine. TheAbbreviations: AA, all-atom; AoC, Aspergillus oryzae cutinase; AOT, sodium bis(2-ethylhexyl) sulfosuccinate; cmc, critical micelle concentration; DEP, diethylphosphate; DNPP, diethyl p-nitrophenyl phosphate; EDTA, ethylene diamine tetraacetate; FsC, Fusarium solani cutinase; GcC, Glomerella cingulata cutinase; HiC, Humicola insolens cutinase; HSQC, heteronuclear singlequantum coherence; IPTG, isopropyl b-D-1-thiogalactopyranoside; ITC, isothermal titration calorimetry; MD, molecular dynamics; MEP, monoethylphosphate; MWCO, molecular weight cut-off; PAGE, polyacrylamide gel electrophoresis; RMSD, root mean square deviation; RMSF, root mean square fluctuation; TES, N-[tris(hydroxymethyl)methyl]-2-aminoethanesulfonic acid; SANS, small-angle neutron scattering; SDS, sodium dodecyl sulfate.Additional Supporting Information may be found in the online version of this article.An interactive view is available in the electronic version of the article. enzyme has the same fold as reported for other cutinases but, unexpectedly, esterification of the active site serine is accompanied by the ethylation of the active site histidine which flips out from its usual position in the triad.

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Presenting your structures: theCCP4mgmolecular-graphics software

Abstract: The CCP4 molecular-graphics program now uses the Qt framework to provide a modern look and feel. There are many new features including rendering for publication-quality images and sequence alignment.

Cited by 1,199 publications

References 36 publications

Haemophilus influenzae stores and distributes hemin by using Protein E

Haemophilus influenzae stores and distributes hemin by using Protein E

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution

Thermodynamic and structural investigation of the specific SDS binding of humicola insolens cutinase

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