scholarly journals Ancestral L-amino acid oxidases for deracemization and stereoinversion of amino acids

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Shogo Nakano ◽  
Kohei Kozuka ◽  
Yuki Minamino ◽  
Hiroka Karasuda ◽  
Fumihito Hasebe ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Engineering ◽  
Crystal Structures ◽  
Reaction Mechanisms ◽  
Molecular Level ◽  
Substrate Recognition ◽  
Engineering Method ◽  
Substrate Selectivity ◽  
X Ray

AbstractL-amino acid oxidases (LAAOs) can be applied to convert racemic amino acids to D-isomers, which are potential precursors of pharmaceuticals. However, this application is hampered by the lack of available stable and structure-determined LAAOs. In this study, we attempt to address this limitation by utilizing two ancestral LAAOs: AncLAAO-N4 and AncLAAO-N5. AncLAAO-N4 has the highest thermal and temporal stabilities among the designed LAAOs that can be used for deracemization and stereoinversion. AncLAAO-N5 can provide X-ray crystal structures, which are helpful to reveal substrate recognition and reaction mechanisms of LAAOs at the molecular level. Next, we attempted to improve activity of AncLAAO-N4 toward L-Val through a semi-rational protein engineering method. Three variants with enhanced activity toward L-Val were obtained. Taken together, we believe that the activity and substrate selectivity of AncLAAOs give them the potential to be key enzymes in various chemoenzymatic reactions.

X-ray studies on crystalline complexes involving amino acids and peptides. XL. Conformational variability, recurring and new features of aggregation, and effect of chirality in the malonic acid complexes of DL- and L-arginine

2002 ◽  
Vol 58 (6) ◽  
pp. 1051-1056 ◽  
Author(s):  
N. T. Saraswathi ◽  
M. Vijayan
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonding ◽  
Amino Acid ◽  
Crystal Structures ◽  
Malonic Acid ◽  
Conformational Flexibility ◽  
X Ray ◽  
Conformational Variability ◽  
Aggregation Pattern ◽  
Positively Charged

The crystal structures of the complexes of malonic acid with DL- and L-arginine, which contain positively charged argininium ions and negatively charged semimalonate ions, further demonstrate the conformational flexibility of amino acids. A larger proportion of folded conformations than would be expected on the basis of steric consideration appears to occur in arginine, presumably because of the requirements of hydrogen bonding. The aggregation pattern in the DL-arginine complex bears varying degrees of resemblance to patterns observed in other similar structures. An antiparallel hydrogen-bonded dimeric arrangement of arginine, and to a lesser extent lysine, is a recurring motif. Similarities also exist among the structures in the interactions with this motif and its assembly into larger features of aggregation. However, the aggregation pattern observed in the L-arginine complex differs from any observed so far, which demonstrates that all the general patterns of amino-acid aggregation have not yet been elucidated. The two complexes represent cases where the reversal of the chirality of half the amino-acid molecules leads to a fundamentally different aggregation pattern.

Crystal structures of non-proteinogenic amino acid peroxosolvates: rare example of H-bonded hydrogen peroxide chains

CrystEngComm ◽  
2018 ◽  
Vol 20 (46) ◽  
pp. 7413-7416 ◽  
Author(s):  
Mger A. Navasardyan ◽  
Dmitry A. Grishanov ◽  
Tatiana A. Tripol'skaya ◽  
Lyudmila G. Kuz'mina ◽  
Petr V. Prikhodchenko ◽  
...  
Keyword(s):  
Amino Acids ◽  
Hydrogen Peroxide ◽  
Amino Acid ◽  
Crystal Structures ◽  
Proteinogenic Amino Acid ◽  
X Ray ◽  
X Ray Crystallography

Novel peroxosolvates of the non-proteinogenic amino acids sarcosine C3H7NO2·H2O2 (1) and phenylserine C9H11NO3·H2O2 (2) were prepared and their structures were determined by X-ray crystallography.

Developing structure-based models to predict substrate specificity of D-group (Type II) molybdenum enzymes: application to a molybdo-enzyme of unknown function from Archaeoglobus fulgidus

2006 ◽  
Vol 34 (1) ◽  
pp. 118-121 ◽  
Author(s):  
E.J. Dridge ◽  
D.J. Richardson ◽  
R.J. Lewis ◽  
C.S. Butler
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Archaeoglobus Fulgidus ◽  
Substrate Selectivity ◽  
Type Ii ◽  
Amino Acid Residues ◽  
Sequence Alignments ◽  
X Ray ◽  
Group Type

The AF0174–AF0176 gene cluster in Archaeoglobus fulgidus encodes a putative oxyanion reductase of the D-type (Type II) family of molybdo-enzymes. Sequence analysis reveals that the catalytic subunit AF0176 shares low identity (31–32%) and similarity (41–42%) to both NarG and SerA, the catalytic components of the respiratory nitrate and selenate reductases respectively. Consequently, predicting the oxyanion substrate selectivity of AF0176 has proved difficult based solely on sequence alignments. In the present study, we have modelled both AF0176 and SerA on the recently determined X-ray structure of the NAR (nitrate reductase) from Escherichia coli and have identified a number of key amino acid residues, conserved in all known NAR sequences, including AF0176, that we speculate may enhance selectivity towards trigonal planar (NO3−) rather than tetrahedral (SeO42− and ClO4−) substrates.

Chiral Ferrocene Amines Derived from Amino Acids and Peptides:  Synthesis, Solution and X-ray Crystal Structures and Electrochemical Investigations

2000 ◽  
Vol 39 (24) ◽  
pp. 5437-5443 ◽  
Author(s):  
Alexandra Hess ◽  
Jan Sehnert ◽  
Thomas Weyhermüller ◽  
Nils Metzler-Nolte
Keyword(s):  
Amino Acids ◽  
Crystal Structures ◽  
X Ray ◽  
Peptides Synthesis ◽  
Synthesis Solution

Structural characterization of folded and extended conformations in peptides containing γ amino acids with proteinogenic side chains: crystal structures of γn, (αγ)n and γγδγ sequences

2015 ◽  
Vol 39 (5) ◽  
pp. 3319-3326 ◽  
Author(s):  
Madhusudana M. B. Reddy ◽  
K. Basuroy ◽  
S. Chandrappa ◽  
B. Dinesh ◽  
B. Vasantha ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Crystal Structures ◽  
Structural Characterization ◽  
Side Chains ◽  
Amino Acid Residues

γn amino acid residues can be incorporated into structures in γn and hybrid sequences containing folded and extended α and δ residues.

scholarly journals Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

2020 ◽  
Vol 117 (20) ◽  
pp. 10806-10817 ◽  
Author(s):  
Michael P. Torrens-Spence ◽  
Ying-Chih Chiang ◽  
Tyler Smith ◽  
Maria A. Vicent ◽  
Yi Wang ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Convergent Evolution ◽  
Structural Features ◽  
Divergent Evolution ◽  
Structural Basis ◽  
Acid Decarboxylase ◽  
Substrate Selectivity ◽  
Amino Acid Decarboxylase ◽  
Catalytic Mechanisms

Radiation of the plant pyridoxal 5′-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

Sorption of α-amino-acids by copper montmorillonite

Clay Minerals ◽  
1967 ◽  
Vol 7 (2) ◽  
pp. 167-176 ◽  
Author(s):  
W. Bodenheimer ◽  
L. Heller
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Complex Formation ◽  
Glutamic Acid ◽  
Acid Complex ◽  
X Ray ◽  
Ray Methods

AbstractSorption of an acidic, amphoteric, sulphur containing and basic α-amino-acid (glutamic acid, glycine, methionine and lysine) by copper montmorillonite was studied by chemical and X-ray methods. With glutamic acid complex formation occurs only in solution but increasing basicity of the aminoacid favours complex formation in the clay interlayers.

Conformational study of the 3,6-dihydro-2H-1,4-oxazin-2-one fragment in 8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione stereoisomers

2017 ◽  
Vol 73 (7) ◽  
pp. 556-562
Author(s):  
Ewa Żesławska ◽  
Anna Jakubowska ◽  
Wojciech Nitek
Keyword(s):  
Amino Acids ◽  
Crystal Structures ◽  
Stereoselective Synthesis ◽  
Biologically Active ◽  
Asymmetric Unit ◽  
Conformational Study ◽  
X Ray Diffraction ◽  
X Ray ◽  
Natural Amino Acids ◽  
Heterocyclic Moiety

Unnatural cyclic α-amino acids play an important role in the search for biologically active compounds and macromolecules. Enantiomers of natural amino acids with a D configuration are not naturally encoded, but can be chemically synthesized. The crystal structures of two enantiomers obtained by a method of stereoselective synthesis, namely (5R,8S)-8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione, (1), and (5S,8R)-8-tert-butyl-7-methoxy-8-methyl-9-oxa-6-azaspiro[4.5]decane-2,10-dione, (2), both C14H21NO4, were determined by X-ray diffraction. Both enantiomers crystallize isostructurally in the space group P21, with one molecule in the asymmetric unit and with the same packing motif. The crystal structures are stabilized by C—H...O hydrogen bonds, resulting in the formation of chains along the [100] and [010] directions. The conformation of the 3,6-dihydro-2H-1,4-oxazin-2-one fragment was compared with other crystal structures possessing this heterocyclic moiety. The comparison showed that the title compounds are not exceptional among structures containing the 3,6-dihydro-2H-1,4-oxazin-2-one fragment. The planar moiety was more frequently observed in derivatives in which this fragment was not condensed with other rings.

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