scholarly journals Crystal Structures of the Ferrous Dioxygen Complex of Wild-type Cytochrome P450eryF and Its Mutants, A245S and A245T

2005 ◽  
Vol 280 (23) ◽  
pp. 22102-22107 ◽  
Author(s):  
Shingo Nagano ◽  
Jill R. Cupp-Vickery ◽  
Thomas L. Poulos
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Crystal Structures ◽  
Proton Donor ◽  
Initial Structure ◽  
Hydrogen Bond Network ◽  
Wild Type ◽  
In The Wild ◽  
Site Water ◽  
Bond Network

Cytochrome P450eryF (CYP107A) from Saccaropolyspora ertherea catalyzes the hydroxylation of 6-deoxyerythronolide B, one of the early steps in the biosynthesis of erythromycin. P450eryF has an alanine rather than the conserved threonine that participates in the activation of dioxygen (O2) in most other P450s. The initial structure of P450eryF (Cupp-Vickery, J. R., Han, O., Hutchinson, C. R., and Poulos, T. L. (1996) Nat. Struct. Biol. 3, 632–637) suggests that the substrate 5-OH replaces the missing threonine OH group and holds a key active site water molecule in position to donate protons to the iron-linked dioxygen, a critical step for the monooxygenase reaction. To probe the proton delivery system in P450eryF, we have solved crystal structures of ferrous wild-type and mutant (Fe2+) dioxygen-bound complexes. The catalytic water molecule that was postulated to provide protons to dioxygen is absent, although the substrate 5-OH group donates a hydrogen bond to the iron-linked dioxygen. The hydrogen bond network observed in the wild-type ferrous dioxygen complex, water 63-Glu360-Ser246-water 53-Ala241 carbonyl in the I-helix cleft, is proposed as the proton transfer pathway. Consistent with this view, the hydrogen bond network in the O2·A245S and O2 ·A245T mutants, which have decreased or no enzyme activity, was perturbed or disrupted, respectively. The mutant Thr245 side chain also perturbs the hydrogen bond between the substrate 5-OH and dioxygen ligand. Contrary to the previously proposed mechanism, these results support the direct involvement of the substrate in O2 activation but raise questions on the role water plays as a direct proton donor to the iron-linked dioxygen.

Halides of Macrocyclic Silver(II) Complexes: Crystal Structures with Hydrogen Bond Network and Reaction Kinetics of the Decomposition

2021 ◽  
pp. 120431
Author(s):  
Akinori Honda ◽  
Shunta Kakihara ◽  
Shuhei Ichimura ◽  
Kazuaki Tomono ◽  
Mina Matsushita ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Reaction Kinetics ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Kinetics Of

Supramolecular assembling using synthons with NH—CO(S)—CS—NH and NH—CO—CO—NH functionalities: crystal structures of (S,S)-N,N′-monothiooxalyldileucine methyl ester and its dithio analogue

2004 ◽  
Vol 60 (1) ◽  
pp. 90-96 ◽  
Author(s):  
Biserka Kojić-Prodić ◽  
Berislav Perić ◽  
Zoran Štefanić ◽  
Anton Meden ◽  
Janja Makarević ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Methyl Ester ◽  
Crystal Structures ◽  
Hydrogen Bond Network ◽  
Asymmetric Unit ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
Bond Network ◽  
Bonding Systems

To compare the structural properties of oxalamide and thiooxalamide groups in the formation of hydrogen bonds suitable for supramolecular assemblies a series of retropeptides was studied. Some of them, having oxalamide bridges, are gelators of organic solvents and water. However, retropeptides with oxygen replaced by the sp 2 sulfur have not exhibited such properties. The crystal structures of the two title compounds are homostructural, i.e. they have similar packing arrangements. The monothio compound crystallizes in the orthorhombic space group P212121 with two molecules in the asymmetric unit arranged in a hydrogen-bond network with an approximate 41 axis along the crystallographic b axis. However, the dithio and dioxo analogues crystallize in the tetragonal space group P41 with similar packing patterns and hydrogen-bonding systems arranged in agreement with a crystallographic 41 axis. Thus, these two analogues are isostructural having closely related hydrogen-bonding patterns in spite of the different size and polarity of oxygen and sulfur which serve as the proton acceptors.

Tautomerism and hydrogen bonding in guaninium phosphite and guaninium phosphate salts

2007 ◽  
Vol 63 (3) ◽  
pp. 448-458 ◽  
Author(s):  
El-Eulmi Bendeif ◽  
Slimane Dahaoui ◽  
Nourredine Benali-Cherif ◽  
Claude Lecomte
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Monoclinic Space Group ◽  
Data Sets ◽  
Hydrogen Bond Network ◽  
Space Group ◽  
X Ray ◽  
Bond Network ◽  
Phosphate Salts

The crystal structures of three similar guaninium salts, guaninium monohydrogenphosphite monohydrate, C5H6N5O+·H2O3P−·H2O, guaninium monohydrogenphosphite dihydrate, C5H6N5O+·H2O3P−·2H2O, and guaninium dihydrogenmonophosphate monohydrate, C5H6N5O+·H2O4P−·H2O, are described and compared. The crystal structures have been determined from accurate single-crystal X-ray data sets collected at 100 (2) K. The two phosphite salts are monoclinic, space group P21/c, with different packing and the monophosphate salt is also monoclinic, space group P21/n. An investigation of the hydrogen-bond network in these guaninium salts reveals the existence of two ketoamine tautomers, the N9H form and an N7H form.

The Role of a Conserved Internal Water Molecule and Its Associated Hydrogen Bond Network in Cytochrfome c

1994 ◽  
Vol 236 (3) ◽  
pp. 786-799 ◽  
Author(s):  
Albert M. Berghuis ◽  
J.Guy Guillemette ◽  
George McLendon ◽  
Fred Sherman ◽  
Michael Smith ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Water Molecule ◽  
Hydrogen Bond Network ◽  
Internal Water ◽  
Bond Network

scholarly journals Crystal structure of a calcium(II)–pyrroloquinoline quinone (PQQ) complex outside a protein environment

2020 ◽  
Vol 76 (12) ◽  
pp. 1051-1056
Author(s):  
Henning Lumpe ◽  
Peter Mayer ◽  
Lena J. Daumann
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Crystal Structures ◽  
Pyrroloquinoline Quinone ◽  
Crystal Structure Analysis ◽  
Hydrogen Bond Network ◽  
Alcohol Dehydrogenases ◽  
Bond Network ◽  
Similarities And Differences ◽  
Protein Environment

Pyrroloquinoline quinone (PQQ) is an important cofactor of calcium- and lanthanide-dependent alcohol dehydrogenases, and has been known for over 30 years. Crystal structures of Ca–MDH enzymes (MDH is methanol dehydrogenase) have been known for some time; however, crystal structures of PQQ with biorelevant metal ions have been lacking in the literature for decades. We report here the first crystal structure analysis of a Ca–PQQ complex outside the protein environment, namely, poly[[undecaaquabis(μ-4,5-dioxo-4,5-dihydro-1H-pyrrolo[2,3-f]quinoline-2,7,9-tricarboxylato)tricalcium(II)] dihydrate], {[Ca3(C14H3N2O8)2(H2O)11]·2H2O} n . The complex crystallized as Ca3PQQ2·13H2O with Ca2+ in three different positions and PQQ3−, including an extensive hydrogen-bond network. Similarities and differences to the recently reported structure with biorelevant europium (Eu2PQQ2) are discussed.

scholarly journals Cryo-EM structures of α-synuclein fibrils with the H50Q hereditary mutation reveal new polymorphs

2019 ◽  
Author(s):  
David R. Boyer ◽  
Binsen Li ◽  
Chuanqi Sun ◽  
Weijia Fan ◽  
Michael R. Sawaya ◽  
...  
Keyword(s):  
Parkinson’S Disease ◽  
Hydrogen Bond ◽  
Parkinson's Disease ◽  
Dementia With Lewy Bodies ◽  
Amyloid Fibrils ◽  
Lewy Bodies ◽  
Wild Type ◽  
In The Wild ◽  
Bond Network ◽  
Intramolecular Hydrogen

AbstractDeposits of amyloid fibrils of α-synuclein are the histological hallmarks of Parkinson’s disease, multiple system atrophy, and dementia with Lewy bodies. Although most cases of these diseases are sporadic, autosomal-dominant hereditary mutations have been linked to Parkinson’s disease and dementia with Lewy bodies. Seeing the changes to the structure of amyloid fibrils bearing these mutations may help to understand these diseases. To this end, we determined the cryo-EM structures of α-synuclein fibrils containing the H50Q hereditary mutation. We find that the H50Q mutation results in two new polymorphs of α-synuclein, which we term Narrow and Wide Fibrils. Both polymorphs recapitulate the conserved kernel formed by residues 50-77 observed in wild-type structures; however, the Narrow and Wide Fibrils reveal that H50Q disrupts a key interaction between H50-E57 on the opposing protofilament, abolishing the extensive protofilament interface formed by preNAC residues in the wild-type “rod” structure. Instead, the Narrow Fibril is formed from a single protofilament and the two protofilaments of the Wide protofilament are held together by only a pair of atoms – the Cɣ atoms from the two threonine 59 sidechains. Further, we find that H50Q forms an intramolecular hydrogen bond with K45 leading to the formation of a novel β-arch formed by residues 36-46 that features an extensive hydrogen-bond network between Y39, T44, and E46. The structures of the H50Q polymorphs help to rationalize the faster aggregation kinetics, higher seeding capacity in biosensor cells, and greater cytotoxicity we observe for H50Q compared to wild-type α-synuclein.

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