The Crystal Structures of Thermomyces (Humicola) Lanuginosa Lipase in Complex with Enzymatic Reactants

2020 ◽  
Vol 16 (3) ◽  
pp. 199-213 ◽  
Author(s):  
Alexander McPherson ◽  
Steven B. Larson ◽  
Andrew Kalasky
Keyword(s):  
Active Form ◽  
Water Interface ◽  
Asymmetric Unit ◽  
Threefold Axis ◽  
Crystal Forms ◽  
Space Groups ◽  
Interfacial Activation ◽  
X Ray Crystallography ◽  
Fatty Acid Chain ◽  
Chain Lengths

Aim: To understand the details of the action of fungal lipase and the mechanism for its observed interfacial activation. Background: Fungal lipase, crucial to biotechnology, functions at the lipid - water interface where it undergoes a poorly understood interfacial activation. Biochemical factors influencing its activation and inhibition are also poorly understood. This study provides a basis for its activity and a plausible mechanism for interfacial activation. Objective: To determine the structures of fungal lipase in different crystal forms in complex with their enzymatic reactants and inhibitors. Method: X-ray crystallography. Results: Thermomyces lanuginosa lipase was visualized in three crystal forms, of space groups H32, P21 and I222 at 1.3 to 1.45 Å resolution. Rhombohedral crystals have one molecule, lacking segment 241 to 252, as an asymmetric unit, with molecules organized as two trimers. Monoclinic crystals’ asymmetric unit is six intact molecules organized as two, nearly identical trimers, each exhibiting an NCS threefold axis. The “lid” helix was consistently closed. Oligomerization into trimers creates an internal hydrophobic cavity where catalysis occurs. In monoclinic and orthorhombic crystals, active site serines were esterified to fatty acids. Lipase had bound within their trimeric, hydrophobic cavities 1,3-diacylglycerols with fatty acid chain lengths of about 18 carbons. Conclusions: Results suggest trimers are likely the active form of the enzyme at the lipid-water interface. Formation of trimers may provide an explanation for “interfacial activation”.

Crystal Structures of and Polarized Absorption-Spectroscopy in Racemic and Resolved [Ru(bpy)3] (ClO4)2 and [Zn(bpy)3] (ClO4)2Bpy=2,2'-Bipyridine

1995 ◽  
Vol 48 (5) ◽  
pp. 929 ◽  
Author(s):  
E Krausz ◽  
H Riesen ◽  
AD Rae
Keyword(s):  
Room Temperature ◽  
Energy Difference ◽  
Temperature Structure ◽  
Asymmetric Unit ◽  
Threefold Axis ◽  
Crystal Forms ◽  
The Third ◽  
Racemic Form ◽  
Ligand Charge Transfer ◽  
Dominant Influence

[Zn( bpy )3] (ClO4)2 and [ Ru ( bpy )3] (ClO4)2 are isomorphous in both their racemic and resolved crystal forms. The resolved materials are monohydrates and have a C 2, Z = 8, structure with two independent formula units on general sites in the asymmetric unit. The cations have the same chirality. The inherent threefold axis of each cation lies approximately parallel to the c axis. The unrelated racemic form has a C2/c, Z = 4, structure which is a commensurate modulation of a P3c1, Z = 2, parent structure, typified by the room-temperature structure of [ Ru ( bpy )3] (PF6)2. A primary, secondary and tertiary axis of P3c1 become the c, b and a axes respectively of C2/c, retaining a third of the symmetry elements of P3c1. The crystals grow as multiply contacted twins. This structure bas just one spectroscopic site with the cation lying on a twofold axis that passes through the metal and one of the bidendate ligands and relates the other two ligands to each other. This feature is particularly useful in the study of the optical spectroscopy of the metal-to- ligand charge transfer excitations of [ Ru ( bpy )3]2+ and related systems. A comparison of structural and spectral data indicates that the positions of the anions have a dominant influence on the relative energies of the metal-to- ligand excitations. An energy difference between excitations involving the two (lower-energy) equivalent ligands and the third ligand of the order of 800 cm-1 is indicated in both singlet and triplet regions for the racemic perchlorate. The absorption spectra of [ Ru ( bpy )3]2+and [Os( bpy )3]2+ in a number of crystalline hosts are compared and discussed.

scholarly journals Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity

2021 ◽  
Vol 22 (9) ◽  
pp. 4769
Author(s):  
Pablo Maturana ◽  
María S. Orellana ◽  
Sixto M. Herrera ◽  
Ignacio Martínez ◽  
Maximiliano Figueroa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Conformational Dynamics ◽  
High Specificity ◽  
Arginine Decarboxylase ◽  
Space Groups ◽  
X Ray Crystallography ◽  
High Dynamics ◽  
Dynamics Simulations

Agmatine is the product of the decarboxylation of L-arginine by the enzyme arginine decarboxylase. This amine has been attributed to neurotransmitter functions, anticonvulsant, anti-neurotoxic, and antidepressant in mammals and is a potential therapeutic agent for diseases such as Alzheimer’s, Parkinson’s, and cancer. Agmatinase enzyme hydrolyze agmatine into urea and putrescine, which belong to one of the pathways producing polyamines, essential for cell proliferation. Agmatinase from Escherichia coli (EcAGM) has been widely studied and kinetically characterized, described as highly specific for agmatine. In this study, we analyze the amino acids involved in the high specificity of EcAGM, performing a series of mutations in two loops critical to the active-site entrance. Two structures in different space groups were solved by X-ray crystallography, one at low resolution (3.2 Å), including a guanidine group; and other at high resolution (1.8 Å) which presents urea and agmatine in the active site. These structures made it possible to understand the interface interactions between subunits that allow the hexameric state and postulate a catalytic mechanism according to the Mn2+ and urea/guanidine binding site. Molecular dynamics simulations evaluated the conformational dynamics of EcAGM and residues participating in non-binding interactions. Simulations showed the high dynamics of loops of the active site entrance and evidenced the relevance of Trp68, located in the adjacent subunit, to stabilize the amino group of agmatine by cation-pi interaction. These results allow to have a structural view of the best-kinetic characterized agmatinase in literature up to now.

The effect of partial methylation of the glycine amino group on crystal structure inN,N-dimethylglycine and its hemihydrate

2012 ◽  
Vol 68 (8) ◽  
pp. o283-o287 ◽  
Author(s):  
Vasily S. Minkov ◽  
Elena V. Boldyreva
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Water Molecules ◽  
Amino Group ◽  
Asymmetric Unit ◽  
Partial Methylation ◽  
Space Groups ◽  
Carboxylate Groups ◽  
Anhydrous Compound ◽  
Additional Hydrogen

N,N-Dimethylglycine, C4H9NO2, and its hemihydrate, C4H9NO2·0.5H2O, are discussed in order to follow the effect of the methylation of the glycine amino group (and thus its ability to form several hydrogen bonds) on crystal structure, in particular on the possibility of the formation of hydrogen-bonded `head-to-tail' chains, which are typical for the crystal structures of amino acids and essential for considering amino acid crystals as mimics of peptide chains. Both compounds crystallize in centrosymmetric space groups (PbcaandC2/c, respectively) and have twoN,N-dimethylglycine zwitterions in the asymmetric unit. In the anhydrous compound, there are no head-to-tail chains but the zwitterions formR44(20) ring motifs, which are not bonded to each other by any hydrogen bonds. In contrast, in the crystal structure ofN,N-dimethylglycinium hemihydrate, the zwitterions are linked to each other by N—H...O hydrogen bonds into infiniteC22(10) head-to-tail chains, while the water molecules outside the chains provide additional hydrogen bonds to the carboxylate groups.

Structural studies of complexes of kallikrein 4 with wild-type and mutated forms of the Kunitz-type inhibitor BbKI

2021 ◽  
Vol 77 (8) ◽  
Author(s):  
Mi Li ◽  
Jaroslav Srp ◽  
Michael Mareš ◽  
Alexander Wlodawer ◽  
Alla Gustchina
Keyword(s):  
Serine Proteases ◽  
Structural Studies ◽  
Wild Type ◽  
Inhibitory Potency ◽  
Crystal Forms ◽  
Space Groups ◽  
Bovine Trypsin ◽  
Kallikrein 4 ◽  
Kunitz Type ◽  
Resolution Structure

Structures of BbKI, a recombinant Kunitz-type serine protease inhibitor from Bauhinia bauhinioides, complexed with human kallikrein 4 (KLK4) were determined at medium-to-high resolution in four crystal forms (space groups P3121, P6522, P21 and P61). Although the fold of the protein was virtually identical in all of the crystals, some significant differences were observed in the conformation of Arg64 of BbKI, the residue that occupies the S1 pocket in KLK4. Whereas this residue exhibited two orientations in the highest resolution structure (P3121), making either a canonical trypsin-like interaction with Asp189 of KLK4 or an alternate interaction, only a single alternate orientation was observed in the other three structures. A neighboring disulfide, Cys191–Cys220, was partially or fully broken in all KLK4 structures. Four variants of BbKI in which Arg64 was replaced by Met, Phe, Ala and Asp were expressed and crystallized, and their structures were determined in complex with KLK4. Structures of the Phe and Met variants complexed with bovine trypsin and of the Phe variant complexed with α-chymotrypsin were also determined. Although the inhibitory potency of these variant forms of BbKI was lowered by up to four orders of magnitude, only small changes were seen in the vicinity of the mutated residues. Therefore, a totality of subtle differences in KLK4–BbKI interactions within the fully extended interface in the structures of these variants might be responsible for the observed effect. Screening of the BbKI variants against a panel of serine proteases revealed an altered pattern of inhibitory specificity, which was shifted towards that of chymotrypsin-like proteases for the hydrophobic Phe and Met P1 substitutions. This work reports the first structures of plant Kunitz inhibitors with S1-family serine proteases other than trypsin, as well as new insights into the specificity of inhibition of medically relevant kallikreins.

3(5),4-Dimethyl- and 3,4,5-trimethylpyrazole at 200 K. X-ray crystallography and quantum-chemical analysis

1999 ◽  
Vol 55 (3) ◽  
pp. 441-447 ◽  
Author(s):  
Lourdes Infantes ◽  
Concepción Foces-Foces ◽  
Jose Elguero
Keyword(s):  
Quantum Chemical ◽  
Molecular Structures ◽  
Asymmetric Unit ◽  
Quantum Chemical Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
Crystal And Molecular Structures ◽  
Unit Form ◽  
Proton Disorder ◽  
Independent Molecules

The crystal and molecular structures of 3(5),4-dimethylpyrazole, C5H8N2, (I), and of 3,4,5-trimethylpyrazole, C6H10N2, (II), have been determined at 200 K. In (I) the 4,5-dimethylpyrazole tautomer is present in the solid state and the six independent molecules in the asymmetric unit form trimers via NH...N hydrogen bonds related by a pseudo centre of symmetry. The asymmetric unit of (II) contains one and a half molecules: these exhibit NH proton disorder and are hydrogen bonded to each other via their respective NH groups to form chains. Ab initio calculations at HF and B3LYP/6-31G** levels indicate that the 3,4-dimethylpyrazole tautomer is more stable than the 4,5-dimethylpyrazole tautomer by only approximately 0.5  kcal  mol−1 (1 kcal mol−1 = 4.184 kJ mol−1).

Preliminary crystallographic studies on glutamine synthetase from Mycobacterium tuberculosis

1999 ◽  
Vol 55 (4) ◽  
pp. 865-868 ◽  
Author(s):  
Harindarpal S. Gill ◽  
Gaston M.U. Pfluegl ◽  
David Eisenberg
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Glutamine Synthetase ◽  
Etiologic Agent ◽  
Asymmetric Unit ◽  
Crystal Forms ◽  
X Ray ◽  
Cell Dimensions ◽  
The One ◽  
Unit Cell Dimensions ◽  
Axes Of Symmetry

The etiologic agent of tuberculosis, Mycobacterium tuberculosis, has been shown to secrete the enzyme glutamine synthetase (TB-GS) which is apparently essential for infection. Four crystal forms of a recombinant TB-GS were grown. The one chosen for synchrotron X-ray data collection belongs to space group P212121 with unit-cell dimensions 208 × 258 × 274 Å, yielding 2.4 Å resolution data. A Matthews number of 2.89 Å3 Da−1 is found, corresponding to 24 subunits of molecular mass 1300 kDa in the asymmetric unit. From earlier work, the structure of Salmonella typhimurium GS, which is 51% identical in sequence to TB-GS, is known to be dodecameric with 622 symmetry. Self-rotation calculations on the TB-GS X-ray data reveal only one set of sixfold and twofold axes of symmetry. A Patterson map calculated from the native X-ray data confirms that there are two dodecamers in the asymmetric unit, having both their sixfold and twofold axes parallel to one another.

Substituent position effect on the crystal structures of N-phenyl-2-phthalimidoethanesulfonamide derivatives

2018 ◽  
Vol 74 (1) ◽  
pp. 31-36
Author(s):  
Resul Sevinçek ◽  
Duygu Barut Celepci ◽  
Serap Köktaş Koca ◽  
Özlem Akgül ◽  
Muittin Aygün
Keyword(s):  
Hydrogen Bonds ◽  
Crystal Packing ◽  
Biological Activities ◽  
Position Effect ◽  
Intermolecular Hydrogen Bond ◽  
X Ray ◽  
Space Groups ◽  
X Ray Crystallography ◽  
Hydrogen Bond Interactions ◽  
The Impact

In order to determine the impact of different substituents and their positions on intermolecular interactions and ultimately on the crystal packing, unsubstituted N-phenyl-2-phthalimidoethanesulfonamide, C16H14N2O4S, (I), and the N-(4-nitrophenyl)-, C16H13N3O6S, (II), N-(4-methoxyphenyl)-, C16H16N3O6S, (III), and N-(2-ethylphenyl)-, as the monohydrate, C18H18N2O4S·H2O, (IV), derivatives have been characterized by single-crystal X-ray crystallography. Sulfonamides (I) and (II) have triclinic crystal systems, while (III) and (IV) are monoclinic. Although the molecules differ from each other only with respect to small substituents and their positions, they crystallized in different space groups as a result of differing intra- and intermolecular hydrogen-bond interactions. The structures of (I), (II) and (III) are stabilized by intermolecular N—H...O and C—H...O hydrogen bonds, while that of (IV) is stabilized by intermolecular O—H...O and C—H...O hydrogen bonds. All four structures are of interest with respect to their biological activities and have been studied as part of a program to develop anticonvulsant drugs for the treatment of epilepsy.

scholarly journals Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography

2020 ◽  
Vol 76 (3) ◽  
pp. 322-335 ◽  
Author(s):  
Marta K. Dudek ◽  
Piotr Paluch ◽  
Edyta Pindelska
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Determination ◽  
Structure Prediction ◽  
Structural Features ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
Crystal Forms ◽  
Space Groups ◽  
Nmr Crystallography

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z′ = 1 polymorph (form II), crystallize in P21/c and P 1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z′ = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

Crystallization of the 10-23 DNA enzyme using a combinatorial screen of paired oligonucleotides

1999 ◽  
Vol 55 (11) ◽  
pp. 1885-1892 ◽  
Author(s):  
Jacek Nowakowski ◽  
Peter J. Shim ◽  
Gerald F. Joyce ◽  
C. David Stout
Keyword(s):  
Crystal Formation ◽  
High Quality ◽  
Acid Complex ◽  
Crystal Forms ◽  
X Ray ◽  
X Ray Crystallography ◽  
Crystallization Solution ◽  
Varying Length ◽  
Standard Set

One of the most difficult steps in the X-ray crystallography of nucleic acids is obtaining crystals that diffract to high resolution. The choice of the nucleotide sequence has proven to be more important in producing high-quality crystals than the composition of the crystallization solution. This manuscript describes a systematic procedure for identifying the optimal sizes of a multi-stranded nucleic acid complex which provide high-quality crystals. This approach was used to crystallize the in vitro evolved 10-23 DNA enzyme complexed with its RNA substrate. In less than two months, 81 different enzyme–substrate complexes were generated by combinatorial mixing and annealing of complementary oligonucleotides which differed in length, resulting in duplexes of varying length, with or without nucleotide overhangs. Each of these complexes was screened against a standard set of 48 crystallization conditions and evaluated for crystal formation. The screen resulted in over 40 crystal forms, the best of which diffracted to 2.8 Å resolution when exposed to a synchrotron X-ray source.

scholarly journals aCHESYM: standardized placement of macromolecular models in the unit cell

2014 ◽  
Vol 70 (a1) ◽  
pp. C336-C336
Author(s):  
Marcin Kowiel ◽  
Mariusz Jaskolski ◽  
Andrzej Gzella ◽  
Zbigniew Dauter
Keyword(s):  
Crystal Structures ◽  
Molecular Model ◽  
Unit Cell ◽  
Asymmetric Unit ◽  
Space Groups ◽  
Reflection Data ◽  
Interpretation Errors ◽  
Structure Solution ◽  
Asymmetric Unit Cell ◽  
Atomic Coordinates

Unique choice of the unit cell and the asymmetric unit are well defined and described in the International Tables for Crystallography vol. A. Unfortunately, the placement of molecules within the unit cell is not standardized. Since structure solution programs often use random numbers in their algorithms, the selected set of atomic coordinates may be different even with successive runs of the same program. Although formally correct, an arbitrary choice of molecular placement within the unit cell is confusing and may lead to interpretation errors [1]. With the use of the anti-Cheshire unit cell introduced by Dauter [2], for all space groups without inversion symmetry, it is possible to transform the molecular model such that its center of gravity falls within the anti-Cheshire asymmetric unit cell. It means that for macromolecular crystal structures it should be possible to standardize the placement of the molecules within the unit cell. In consequence, it should be easier for crystallographers and non-crystallographers to compare similar or related crystal structures. An implementation of the anti-Cheshire concept has been programmed in Python as a web service, aCHESYM. The aCHESYM program takes a PDB file as input and transforms the macromolecular model into the desired anti-Cheshire region. The program can also handle structure factor CIF files if the transformation used requires reindexing of the reflection data. The unit cell, coordinates and displacement parameters of all atoms after transformation are saved in a new PDB file. All the calculated transformations are reversible, so there is no danger of data loss. Moreover, the program helps the user to find the most compact assembly of the molecules (chains) in the structure when there are several chains in the asymmetric unit.

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