X-ray Structure ofParamecium bursariaChlorella Virus Arginine Decarboxylase:  Insight into the Structural Basis for Substrate Specificity†

Cobalamin- or B12-dependent radical S-adenosylmethionine (SAM) enzymes acting during carbapenem antibiotic biosynthesis carry out radical-mediated methyl transfers that underlie the therapeutic usefulness of these essential medicines. Here we present x-ray crystal structures of TokK, which are representative of this functional class, containing its two metallocofactors and determined in the presence and absence of carbapenam substrate. The structures give the first visualization of a cobalamin-dependent radical SAM methylase that employs the radical mechanism shared by a vast majority of these enzymes. The structures provide insight into the stereochemistry of initial C6 methylation and suggests that substrate positioning governs the rate of each methylation event.

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RNA polymerase II trapped on a molecular treadmill: Structural basis of persistent transcriptional arrest by a minor groove DNA binder

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2114065119 ◽

2022 ◽

Vol 119 (3) ◽

pp. e2114065119

Author(s):

Juntaek Oh ◽

Tiezheng Jia ◽

Jun Xu ◽

Jenny Chong ◽

Peter B. Dervan ◽

...

Keyword(s):

Rna Polymerase ◽

Rna Polymerase Ii ◽

Minor Groove ◽

Dna Lesions ◽

Structural Basis ◽

Rna Pol Ii ◽

Pol Ii ◽

X Ray ◽

A Minor ◽

Insight Into

Elongating RNA polymerase II (Pol II) can be paused or arrested by a variety of obstacles. These obstacles include DNA lesions, DNA-binding proteins, and small molecules. Hairpin pyrrole-imidazole (Py-Im) polyamides bind to the minor groove of DNA in a sequence-specific manner and induce strong transcriptional arrest. Remarkably, this Py-Im–induced Pol II transcriptional arrest is persistent and cannot be rescued by transcription factor TFIIS. In contrast, TFIIS can effectively rescue the transcriptional arrest induced by a nucleosome barrier. The structural basis of Py-Im–induced transcriptional arrest and why TFIIS cannot rescue this arrest remain elusive. Here we determined the X-ray crystal structures of four distinct Pol II elongation complexes (Pol II ECs) in complex with hairpin Py-Im polyamides as well as of the hairpin Py-Im polyamides–dsDNA complex. We observed that the Py-Im oligomer directly interacts with RNA Pol II residues, introduces compression of the downstream DNA duplex, prevents Pol II forward translocation, and induces Pol II backtracking. These results, together with biochemical studies, provide structural insight into the molecular mechanism by which Py-Im blocks transcription. Our structural study reveals why TFIIS fails to promote Pol II bypass of Py-Im–induced transcriptional arrest.

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Crystal Structure of Human Myotubularin-Related Protein 1 Provides Insight into the Structural Basis of Substrate Specificity

PLoS ONE ◽

10.1371/journal.pone.0152611 ◽

2016 ◽

Vol 11 (3) ◽

pp. e0152611 ◽

Cited By ~ 6

Author(s):

Seoung Min Bong ◽

Kka-bi Son ◽

Seung-Won Yang ◽

Jae-Won Park ◽

Jea-Won Cho ◽

...

Keyword(s):

Crystal Structure ◽

Substrate Specificity ◽

Structural Basis ◽

Related Protein ◽

Insight Into

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Molecular and structural basis for Lewis glycan recognition by a cancer-targeting antibody

Biochemical Journal ◽

10.1042/bcj20200454 ◽

2020 ◽

Vol 477 (17) ◽

pp. 3219-3235

Author(s):

Caroline Soliman ◽

Andrew J. Guy ◽

Jia Xin Chua ◽

Mireille Vankemmelbeke ◽

Richard S. McIntosh ◽

...

Keyword(s):

Cross Reactivity ◽

Structural Basis ◽

Cancer Targeting ◽

Antigen Binding ◽

X Ray ◽

Colorectal Cancer Cells ◽

Structural Details ◽

Dynamics Simulations ◽

Fragment Antigen Binding ◽

Insight Into

Immunotherapy has been successful in treating many tumour types. The development of additional tumour-antigen binding monoclonal antibodies (mAbs) will help expand the range of immunotherapeutic targets. Lewis histo-blood group and related glycans are overexpressed on many carcinomas, including those of the colon, lung, breast, prostate and ovary, and can therefore be selectively targeted by mAbs. Here we examine the molecular and structural basis for recognition of extended Lea and Lex containing glycans by a chimeric mAb. Both the murine (FG88.2) IgG3 and a chimeric (ch88.2) IgG1 mAb variants showed reactivity to colorectal cancer cells leading to significantly reduced cell viability. We determined the X-ray structure of the unliganded ch88.2 fragment antigen-binding (Fab) containing two Fabs in the unit cell. A combination of molecular docking, glycan grafting and molecular dynamics simulations predicts two distinct subsites for recognition of Lea and Lex trisaccharides. While light chain residues were exclusively used for Lea binding, recognition of Lex involved both light and heavy chain residues. An extended groove is predicted to accommodate the Lea–Lex hexasaccharide with adjoining subsites for each trisaccharide. The molecular and structural details of the ch88.2 mAb presented here provide insight into its cross-reactivity for various Lea and Lex containing glycans. Furthermore, the predicted interactions with extended epitopes likely explains the selectivity of this antibody for targeting Lewis-positive tumours.

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Quantitative Analysis Of X-Ray Images From Geological Materials

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010013482x ◽

1990 ◽

Vol 48 (2) ◽

pp. 244-245

Author(s):

J. M. Paque ◽

R. Browning ◽

P. L. King ◽

P. Pianetta

Keyword(s):

Quantitative Analysis ◽

Bulk Composition ◽

Principal Component ◽

Analytical Description ◽

Bulk Sample ◽

Geological Samples ◽

X Ray ◽

Software And Hardware ◽

And Storage ◽

Insight Into

Geological samples typically contain many minerals (phases) with multiple element compositions. A complete analytical description should give the number of phases present, the volume occupied by each phase in the bulk sample, the average and range of composition of each phase, and the bulk composition of the sample. A practical approach to providing such a complete description is from quantitative analysis of multi-elemental x-ray images.With the advances in recent years in the speed and storage capabilities of laboratory computers, large quantities of data can be efficiently manipulated. Commercial software and hardware presently available allow simultaneous collection of multiple x-ray images from a sample (up to 16 for the Kevex Delta system). Thus, high resolution x-ray images of the majority of the detectable elements in a sample can be collected. The use of statistical techniques, including principal component analysis (PCA), can provide insight into mineral phase composition and the distribution of minerals within a sample.

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Electron diffraction detection of ordliking in annealed PbTe thin film

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100178227 ◽

1990 ◽

Vol 48 (4) ◽

pp. 1018-1019

Author(s):

Karimat El-Sayed

Keyword(s):

Thin Film ◽

Electron Diffraction ◽

Lead Telluride ◽

Structural Basis ◽

Face Centered Cubic ◽

X Ray ◽

Polycrystalline Thin Films ◽

Stage Process ◽

Diffraction Patterns ◽

Face Centered

Lead telluride is an important semiconductor of many applications. Many Investigators showed that there are anamolous descripancies in most of the electrophysical properties of PbTe polycrystalline thin films on annealing. X-Ray and electron diffraction studies are being undertaken in the present work in order to explain the cause of this anamolous behaviour.Figures 1-3 show the electron diffraction of the unheated, heated in air at 100°C and heated in air at 250°C respectively of a 300°A polycrystalline PbTe thin film. It can be seen that Fig. 1 is a typical [100] projection of a face centered cubic with unmixed (hkl) indices. Fig. 2 shows the appearance of faint superlattice reflections having mixed (hkl) indices. Fig. 3 shows the disappearance of thf superlattice reflections and the appearance of polycrystalline PbO phase superimposed on the [l00] PbTe diffraction patterns. The mechanism of this three stage process can be explained on structural basis as follows :

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Copper–oxygen Dynamics in Tyrosinase

10.26434/chemrxiv.9255251 ◽

2019 ◽

Author(s):

Nobutaka Fujieda ◽

Sachiko Yanagisawa ◽

Minoru Kubo ◽

Genji Kurisu ◽

Shinobu Itoh

Keyword(s):

Catalytic Mechanism ◽

Substrate Binding ◽

Active Form ◽

Copper Ion ◽

Atomic Resolution ◽

Oxygen Species ◽

X Ray ◽

Oxygen Dynamics ◽

Insight Into ◽

Copper Centre

To unveil the activation of dioxygen on the copper centre (Cu2O2core) of tyrosinase, we performed X-ray crystallograpy with active-form tyrosinase at near atomic resolution. This study provided a novel insight into the catalytic mechanism of the tyrosinase, including the rearrangement of copper-oxygen species as well as the intramolecular migration of copper ion induced by substrate-binding.

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