Crystal structures clarify cofactor binding of plant tyrosine decarboxylase

Fibrillarin (FBL) is an essential and evolutionarily highly conserved S-adenosyl methionine (SAM) dependent methyltransferase. It is the catalytic component of a multiprotein complex that facilitates 2′-O-methylation of ribosomal RNAs (rRNAs), a modification essential for accurate and efficient protein synthesis in eukaryotic cells. It was recently established that human FBL (hFBL) is critical for Nipah, Hendra, and respiratory syncytial virus infections. In addition, overexpression of hFBL contributes towards tumorgenesis and is associated with poor survival in patients with breast cancer, suggesting that hFBL is a potential target for the development of both antiviral and anticancer drugs. An attractive strategy to target cofactor-dependent enzymes is the selective inhibition of cofactor binding, which has been successful for the development of inhibitors against several protein methyltransferases including PRMT5, DOT1L, and EZH2. In this work, we solved crystal structures of the methyltransferase domain of hFBL in apo form and in complex with the cofactor SAM. Screening of a fluorinated fragment library, via X-ray crystallography and 19F NMR spectroscopy, yielded seven hit compounds that competed with cofactor binding, two of which resulted in co-crystal structures. One of these structures revealed unexpected conformational variability in the cofactor binding site, which allows it to accommodate a compound significantly different from SAM. Our structural data provide critical information for the design of selective cofactor competitive inhibitors targeting hFBL, and preliminary elaboration of hit compounds has led to additional cofactor site binders.

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Structural rearrangements occurring upon cofactor binding in the Mycobacterium smegmatis β-ketoacyl-acyl carrier protein reductase MabA

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798318002917 ◽

2018 ◽

Vol 74 (5) ◽

pp. 383-393 ◽

Cited By ~ 3

Author(s):

Tanja Küssau ◽

Marion Flipo ◽

Niel Van Wyk ◽

Albertus Viljoen ◽

Vincent Olieric ◽

...

Keyword(s):

Fatty Acid ◽

Crystal Structures ◽

Active Site ◽

Mycobacterium Smegmatis ◽

Fatty Acid Synthase ◽

Fatty Acid Biosynthesis ◽

Acyl Carrier Protein ◽

Rational Drug Design ◽

Carrier Protein ◽

Cofactor Binding

In mycobacteria, the ketoacyl-acyl carrier protein (ACP) reductase MabA (designated FabG in other bacteria) catalyzes the NADPH-dependent reduction of β-ketoacyl-ACP substrates to β-hydroxyacyl-ACP products. This first reductive step in the fatty-acid biosynthesis elongation cycle is essential for bacteria, which makes MabA/FabG an interesting drug target. To date, however, very few molecules targeting FabG have been discovered and MabA remains the only enzyme of the mycobacterial type II fatty-acid synthase that lacks specific inhibitors. Despite the existence of several MabA/FabG crystal structures, the structural rearrangement that occurs upon cofactor binding is still not fully understood. Therefore, unlocking this knowledge gap could help in the design of new inhibitors. Here, high-resolution crystal structures of MabA from Mycobacterium smegmatis in its apo, NADP+-bound and NADPH-bound forms are reported. Comparison of these crystal structures reveals the structural reorganization of the lid region covering the active site of the enzyme. The crystal structure of the apo form revealed numerous residues that trigger steric hindrance to the binding of NADPH and substrate. Upon NADPH binding, these residues are pushed away from the active site, allowing the enzyme to adopt an open conformation. The transition from an NADPH-bound to an NADP+-bound form is likely to facilitate release of the product. These results may be useful for subsequent rational drug design and/or for in silico drug-screening approaches targeting MabA/FabG.

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Crystal Structures of a Hyperthermophilic Archaeal Homoserine Dehydrogenase Suggest a Novel Cofactor Binding Mode for Oxidoreductases

Scientific Reports ◽

10.1038/srep11674 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 7

Author(s):

Junji Hayashi ◽

Shota Inoue ◽

Kwang Kim ◽

Kazunari Yoneda ◽

Yutaka Kawarabayasi ◽

...

Keyword(s):

Crystal Structures ◽

Binding Mode ◽

Homoserine Dehydrogenase ◽

Cofactor Binding

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Pollutant Identification by Selected Area Electron Diffraction

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100052675 ◽

1974 ◽

Vol 32 ◽

pp. 532-533

Author(s):

R. E. Ferrell ◽

G. G. Paulson ◽

C. W. Walker

Keyword(s):

Thermal Treatment ◽

Electron Diffraction ◽

Sample Preparation ◽

Crystal Structures ◽

Water Samples ◽

Environmental Samples ◽

Short Review ◽

Selected Area Electron Diffraction ◽

Multiple Component

Selected area electron diffraction (SAD) has been used successfully to determine crystal structures, identify traces of minerals in rocks, and characterize the phases formed during thermal treatment of micron-sized particles. There is an increased interest in the method because it has the potential capability of identifying micron-sized pollutants in air and water samples. This paper is a short review of the theory behind SAD and a discussion of the sample preparation employed for the analysis of multiple component environmental samples.

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The Imaging of Crystal Structures and Crystal Defects

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100069995 ◽

1978 ◽

Vol 36 (3) ◽

pp. 207-217

Author(s):

J.M. Cowley

Keyword(s):

Electron Microscope ◽

Crystal Structures ◽

Phase Contrast ◽

Crystal Defects ◽

Atom Density ◽

Lack Of Information ◽

Spatial Frequencies

The problem of "understandinq" electron microscope imaqes becomes more acute as the resolution is improved. The naive interpretation of an imaqe as representinq the projection of an atom density becomes less and less appropriate. We are increasinqly forced to face the complexities of coherent imaqinq of what are essentially phase objects. Most electron microscopists are now aware that, for very thin weakly scatterinq objects such as thin unstained bioloqical specimens, hiqh resolution imaqes are best obtained near the optimum defocus, as prescribed by Scherzer, where the phase contrast imaqe qives a qood representation of the projected potential, apart from a lack of information on the lower spatial frequencies. But phase contrast imaqinq is never simple except in idealized limitinq cases.

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Transmission electron microscope studies in special ceramics

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100108489 ◽

1978 ◽

Vol 36 (1) ◽

pp. 268-269

Author(s):

A. Zangvil ◽

L.J. Gauckler ◽

G. Schneider ◽

M. Rühle

Keyword(s):

Phase Diagrams ◽

Crystal Structures ◽

Thin Foil ◽

Limited Extent ◽

Complex Materials ◽

X Ray Diffraction ◽

X Ray ◽

Transmission Electron ◽

Electron Microscopes ◽

Lattice Resolution

The use of high temperature special ceramics which are usually complex materials based on oxides, nitrides, carbides and borides of silicon and aluminum, is critically dependent on their thermomechanical and other physical properties. The investigations of the phase diagrams, crystal structures and microstructural features are essential for better understanding of the macro-properties. Phase diagrams and crystal structures have been studied mainly by X-ray diffraction (XRD). Transmission electron microscopy (TEM) has contributed to this field to a very limited extent; it has been used more extensively in the study of microstructure, phase transformations and lattice defects. Often only TEM can give solutions to numerous problems in the above fields, since the various phases exist in extremely fine grains and subgrain structures; single crystals of appreciable size are often not available. Examples with some of our experimental results from two multicomponent systems are presented here. The standard ion thinning technique was used for the preparation of thin foil samples, which were then investigated with JEOL 200A and Siemens ELMISKOP 102 (for the lattice resolution work) electron microscopes.

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Advancing the use of Voronoi–Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs

CrystEngComm ◽

10.1039/d0ce01535k ◽

2021 ◽

Author(s):

Viktor N. Serezhkin ◽

Anton V. Savchenkov

Keyword(s):

Crystal Structures ◽

Molecular Crystal ◽

Noncovalent Interactions ◽

Organic Molecular Crystal ◽

Universal Approach ◽

Structure Properties

The universal approach for studying structure/properties relationships shows that every polymorph of galunisertib is characterized with unique noncovalent interactions.

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Crystal structures of Magnaporthe oryzae trehalose-6-phosphate synthase (MoTps1) suggest a model for catalytic process of Tps1

Biochemical Journal ◽

10.1042/bcj20190289 ◽

2019 ◽

Vol 476 (21) ◽

pp. 3227-3240 ◽

Cited By ~ 1

Author(s):

Shanshan Wang ◽

Yanxiang Zhao ◽

Long Yi ◽

Minghe Shen ◽

Chao Wang ◽

...

Keyword(s):

Crystal Structures ◽

Conformational Changes ◽

Magnaporthe Oryzae ◽

Structural Information ◽

Complex Structure ◽

Critical Role ◽

Catalytic Process ◽

Structural Basis ◽

Salt Bridges ◽

Terminal Domain

Trehalose-6-phosphate (T6P) synthase (Tps1) catalyzes the formation of T6P from UDP-glucose (UDPG) (or GDPG, etc.) and glucose-6-phosphate (G6P), and structural basis of this process has not been well studied. MoTps1 (Magnaporthe oryzae Tps1) plays a critical role in carbon and nitrogen metabolism, but its structural information is unknown. Here we present the crystal structures of MoTps1 apo, binary (with UDPG) and ternary (with UDPG/G6P or UDP/T6P) complexes. MoTps1 consists of two modified Rossmann-fold domains and a catalytic center in-between. Unlike Escherichia coli OtsA (EcOtsA, the Tps1 of E. coli), MoTps1 exists as a mixture of monomer, dimer, and oligomer in solution. Inter-chain salt bridges, which are not fully conserved in EcOtsA, play primary roles in MoTps1 oligomerization. Binding of UDPG by MoTps1 C-terminal domain modifies the substrate pocket of MoTps1. In the MoTps1 ternary complex structure, UDP and T6P, the products of UDPG and G6P, are detected, and substantial conformational rearrangements of N-terminal domain, including structural reshuffling (β3–β4 loop to α0 helix) and movement of a ‘shift region' towards the catalytic centre, are observed. These conformational changes render MoTps1 to a ‘closed' state compared with its ‘open' state in apo or UDPG complex structures. By solving the EcOtsA apo structure, we confirmed that similar ligand binding induced conformational changes also exist in EcOtsA, although no structural reshuffling involved. Based on our research and previous studies, we present a model for the catalytic process of Tps1. Our research provides novel information on MoTps1, Tps1 family, and structure-based antifungal drug design.

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