Crystal Structures of a Populus tomentosa 4-Coumarate:CoA Ligase Shed Light on Its Enzymatic Mechanisms

Branching enzyme (BE) is responsible for the third step in glycogen/starch biosynthesis. It catalyzes the cleavage of α-1,4 glucan linkages and subsequent reattachment to form α-1,6 branch points. These branches are crucial to the final structure of glycogen and starch. The crystal structures ofEscherichia coliBE (EcBE) in complex with α-, β- and γ-cyclodextrin were determined in order to better understand substrate binding. Four cyclodextrin-binding sites were identified inEcBE; they were all located on the surface of the enzyme, with none in the vicinity of the active site. While three of the sites were also identified as linear polysaccharide-binding sites, one of the sites is specific for cyclodextrins. In previous work three additional binding sites were identified as exclusively binding linear malto-oligosaccharides. Comparison of the binding sites shed light on this apparent specificity. Binding site IV is located in the carbohydrate-binding module 48 (CBM48) domain ofEcBE and superimposes with the cyclodextrin-binding site found in the CBM48 domain of 5′-AMP-activated protein kinase (AMPK). Comparison of these sites shows the similarities and differences in the two binding modes. While some of the binding sites were found to be conserved between branching enzymes of different organisms, some are quite divergent, indicating both similarities and differences between oligosaccharide binding in branching enzymes from various sources.

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Insights into the van der Waals Radius of Low-Spin Ni(ii) fromMolecular Mechanics Studies and the Crystal Structures of [Ni(cis-cyclohexane-1,3-diamine)2]Cl2, [Ni{(R)-5,5,7-trimethyl-1,4-diazacycloheptane}2]Cl2·H2O and [Ni(5,7-dimethyl-1,4-diazacycloheptane)2](ClO4)2. Synthesis of 5,7-Dimethyl-1,4-diazacycloheptane and an Improved Synthesis of cis-Cyclohexane-1,3-diamine

Australian Journal of Chemistry ◽

10.1071/ch02099 ◽

2002 ◽

Vol 55 (8) ◽

pp. 523 ◽

Cited By ~ 5

Author(s):

V. P. Munk ◽

S. T. Cham ◽

R. R. Fenton ◽

R. K. Hocking ◽

T. W. Hambley

Keyword(s):

Solid State ◽

Molecular Mechanics ◽

Crystal Structures ◽

Van Der Waals ◽

Monoclinic Space Group ◽

Orthorhombic Space Group ◽

Space Group ◽

R Value ◽

Shed Light

The structures of three bis(diamine)nickel(II) complexes, chosen to shed light on the van der Waals radius of nickel(II), are described. [Ni(cis-1,3-chxn)2]Cl2 (cis-1,3-chxn = cis-cyclohexane-1,3-diamine) crystallizes in the monoclinic space group P21/n, with a 6.397(2), b 16.463(4), c 7.229(2) Å, b 90.70(2)�, and its structure has been refined to an R value of 0.031 on 1214F. [Ni{(R)-tmdz}2]Cl2�H2O (tmdz = 5,5,7-trimethyl-1,4-diazacycloheptane) crystallizes in the orthorhombic space group P212121, with a 10.678(1), b 11.073(5), c 17.968(6) Å, and its structure has been refined to an R value of 0.031 on 1586F. [Ni(dmdz)2](ClO4)2 (dmdz = 5,7-dimethyl-1,4-diaza- cycloheptane) crystallizes in the monoclinic space group P21/n, with a 9.582(1), b 10.390(2), c 11.817(3) Å, β 96.19(2)�, and its structure has been refined to an R value of 0.059 on 817F. In all three structures, short Ni��H and Ni��C interactions, ranging from 2.37 to 2.61 Å and 2.99 to 3.03 Å, respectively, are observed. Using molecular mechanics modelling to reproduce these separations, we have arrived at a van der Waals radius of 1.35 Å for low-spin nickel(ii). Analysis of Ni��O contacts in the solid state leads to a van der Waals radius of about 1.26 Å, which is consistent with the molecular mechanics derived value since these are usually longer.

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In vivo pharmacokinetic enhancement of monomeric Fc and monovalent bispecific designs through structural guidance

Communications Biology ◽

10.1038/s42003-021-02565-5 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Lu Shan ◽

Nydia Van Dyk ◽

Nantaporn Haskins ◽

Kimberly M. Cook ◽

Kim L. Rosenthal ◽

...

Keyword(s):

Crystal Structures ◽

Half Life ◽

Fusion Proteins ◽

Molecular Design ◽

Protein Therapeutics ◽

Life Extension ◽

Therapeutic Landscape ◽

Exciting Potential ◽

Shed Light

AbstractIn a biologic therapeutic landscape that requires versatility in targeting specificity, valency and half-life modulation, the monomeric Fc fusion platform holds exciting potential for the creation of a class of monovalent protein therapeutics that includes fusion proteins and bispecific targeting molecules. Here we report a structure-guided approach to engineer monomeric Fc molecules to adapt multiple versions of half-life extension modifications. Co-crystal structures of these monomeric Fc variants with Fc neonatal receptor (FcRn) shed light into the binding interactions that could serve as a guide for engineering the half-life of antibody Fc fragments. These engineered monomeric Fc molecules also enabled the generation of a novel monovalent bispecific molecular design, which translated the FcRn binding enhancement to improvement of in vivo serum half-life.

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The Crystal Structures of Apo and ComplexedSaccharomyces cerevisiaeGNA1 Shed Light on the Catalytic Mechanism of an Amino-sugarN-Acetyltransferase

Journal of Biological Chemistry ◽

10.1074/jbc.m009988200 ◽

2001 ◽

Vol 276 (19) ◽

pp. 16328-16334 ◽

Cited By ~ 54

Author(s):

Caroline Peneff ◽

Dominique Mengin-Lecreulx ◽

Yves Bourne

Keyword(s):

Crystal Structures ◽

Catalytic Mechanism ◽

Shed Light

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New crystal structures of human glutathione transferase A1-1 shed light on glutathione binding and the conformation of the C-terminal helix

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s0907444905039296 ◽

2006 ◽

Vol 62 (2) ◽

pp. 197-207 ◽

Cited By ~ 35

Author(s):

Elin Grahn ◽

Marian Novotny ◽

Emma Jakobsson ◽

Ann Gustafsson ◽

Leif Grehn ◽

...

Keyword(s):

Crystal Structures ◽

Glutathione Transferase ◽

Shed Light ◽

Glutathione Binding

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Elucidation of cladofulvin biosynthesis reveals a cytochrome P450 monooxygenase required for anthraquinone dimerization

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1603528113 ◽

2016 ◽

Vol 113 (25) ◽

pp. 6851-6856 ◽

Cited By ~ 38

Author(s):

Scott Griffiths ◽

Carl H. Mesarich ◽

Benedetta Saccomanno ◽

Abraham Vaisberg ◽

Pierre J. G. M. De Wit ◽

...

Keyword(s):

Cytochrome P450 ◽

Polyketide Synthase ◽

Functional Group ◽

Biological Activities ◽

Large Family ◽

P450 Monooxygenase ◽

Mammalian Cell Lines ◽

Enzymatic Mechanisms ◽

Shed Light

Anthraquinones are a large family of secondary metabolites (SMs) that are extensively studied for their diverse biological activities. These activities are determined by functional group decorations and the formation of dimers from anthraquinone monomers. Despite their numerous medicinal qualities, very few anthraquinone biosynthetic pathways have been elucidated so far, including the enzymatic dimerization steps. In this study, we report the elucidation of the biosynthesis of cladofulvin, an asymmetrical homodimer of nataloe-emodin produced by the fungusCladosporium fulvum. A gene cluster of 10 genes controls cladofulvin biosynthesis, which begins with the production of atrochrysone carboxylic acid by the polyketide synthase ClaG and the β-lactamase ClaF. This compound is decarboxylated by ClaH to yield emodin, which is then converted to chrysophanol hydroquinone by the reductase ClaC and the dehydratase ClaB. We show that the predicted cytochrome P450 ClaM catalyzes the dimerization of nataloe-emodin to cladofulvin. Remarkably, such dimerization dramatically increases nataloe-emodin cytotoxicity against mammalian cell lines. These findings shed light on the enzymatic mechanisms involved in anthraquinone dimerization. Future characterization of the ClaM enzyme should facilitate engineering the biosynthesis of novel, potent, dimeric anthraquinones and structurally related compound families.

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Structural studies on the reaction of isopenicillin N synthase with the substrate analogue delta-(l-alpha-aminoadipoyl)-l-cysteinyl-d-alpha-aminobutyrate

Biochemical Journal ◽

10.1042/bj20021627 ◽

2003 ◽

Vol 372 (3) ◽

pp. 687-693 ◽

Cited By ~ 19

Author(s):

Alexandra J. LONG ◽

Ian J. CLIFTON ◽

Peter L. ROACH ◽

Jack E. BALDWIN ◽

Christopher J. SCHOFIELD ◽

...

Keyword(s):

Crystal Structures ◽

Active Site ◽

Structural Studies ◽

Product Selectivity ◽

Substrate Analogue ◽

Modelling Studies ◽

Key Residues ◽

Haem Iron ◽

Shed Light ◽

Isopenicillin N

Isopenicillin N synthase (IPNS) is a non-haem iron(II) oxidase which catalyses the biosynthesis of isopenicillin N from the tripeptide δ-(l-α-aminoadipoyl)-l-cysteinyl-d-valine (ACV). Herein we report crystallographic studies to investigate the reaction of IPNS with the truncated substrate analogue δ-(l-α-aminoadipoyl)-l-cysteinyl-d-α-aminobutyrate (ACAb). It has been reported previously that this analogue gives rise to three β-lactam products when incubated with IPNS: two methyl penams and a cepham. Crystal structures of the IPNS–Fe(II)–ACAb and IPNS–Fe(II)–ACAb–NO complexes have now been solved and are reported herein. These structures and modelling studies based on them shed light on the diminished product selectivity shown by IPNS in its reaction with ACAb and further rationalize the presence of certain key residues at the IPNS active site.

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