Structural basis for stereospecificity to d-amino acid of glycine oxidase from Bacillus cereus ATCC 14579

The first part of this review deals with the biosynthesis and a biological function of strongly vasoactive peptides named endothelins (ETs) including vasoactive intestinal contractor. Where it was useful, snake venoms sarafotoxins which are structural endothelin derivatives, were also mentioned. In the second part, an attention is paid to structural basis of the ETs biological activity, with respect to alterations of amino acid residues in the parent peptides modifying the conformation and consequently the physico-chemical and biological properties in corresponding ETs analogs. Special attention is focussed on the area of ETs receptors and their interaction with peptide and non peptide agonists and antagonists, important in designing selective inhibitors of ETs receptors potentially applicable as drugs in a medicine. A review with 182 references.

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Structural Basis of Furan-Amino Acid Recognition by a Polyspecific Aminoacyl-tRNA-Synthetase and its Genetic Encoding in Human Cells

ChemBioChem ◽

10.1002/cbic.201402006 ◽

2014 ◽

Vol 15 (12) ◽

pp. 1755-1760 ◽

Cited By ~ 16

Author(s):

Moritz J. Schmidt ◽

Annemarie Weber ◽

Moritz Pott ◽

Wolfram Welte ◽

Daniel Summerer

Keyword(s):

Amino Acid ◽

Trna Synthetase ◽

Human Cells ◽

Structural Basis ◽

Aminoacyl Trna Synthetase ◽

Genetic Encoding ◽

Amino Acid Recognition

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The efficiency of processing and secretion of the thermolysin-like neutral protease from Bacillus cereus does not require the whole prosequence, but does depend on the nature of the amino acid sequence in the region of the cleavage site

Molecular Microbiology ◽

10.1111/j.1365-2958.1994.tb01062.x ◽

1994 ◽

Vol 12 (5) ◽

pp. 747-759 ◽

Cited By ~ 10

Author(s):

Diana R. Wetmore ◽

Sui-Lam Wong ◽

Rodney S. Roche

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Bacillus Cereus ◽

Cleavage Site ◽

Neutral Protease

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Structural Basis for Human Norovirus Capsid Binding to Bile Acids

Journal of Virology ◽

10.1128/jvi.01581-18 ◽

2018 ◽

Vol 93 (2) ◽

Cited By ~ 23

Author(s):

Turgay Kilic ◽

Anna Koromyslova ◽

Grant S. Hansman

Keyword(s):

Bile Acid ◽

Amino Acid ◽

Bile Acids ◽

Natural Infection ◽

Structural Basis ◽

Amino Acid Side Chain ◽

Blood Group Antigens ◽

Human Norovirus ◽

Bile Acid Binding ◽

P Domain

ABSTRACT A recently developed human norovirus cell culture system revealed that the presence of bile enhanced or was an essential requirement for the growth of certain genotypes. Before this discovery, histo-blood group antigens (HBGAs) were the only well-studied cofactor known for human noroviruses, and there was evidence that several genotypes poorly bound HBGAs. Therefore, the purpose of this study was to investigate how human norovirus capsids interact with bile acids. We found that bile acids had low-micromolar affinities for GII.1, GII.10, and GII.19 capsids but did not bind GI.1, GII.3, GII.4, or GII.17. We showed that bile acid bound at a partially conserved pocket on the norovirus capsid-protruding (P) domain using X-ray crystallography. Amino acid sequence alignment and structural analysis delivered an explanation of selective bile acid binding. Intriguingly, we discovered that binding of the bile acid was the critical step to stabilize several P domain loops that optimally placed an essential amino acid side chain (Asp375) to bind HBGAs in an otherwise HBGA nonbinder (GII.1). Furthermore, bile acid enhanced HBGA binding for a known HBGA binder (GII.10). Altogether, these new data suggest that bile acid functions as a loop-stabilizing regulator and enhancer of HBGA binding for certain norovirus genotypes. IMPORTANCE Given that human norovirus virions likely interact with bile acid during a natural infection, our evidence that an HBGA nonbinder (GII.1) can be converted to an HBGA binder after bile acid binding is of major significance. Our data provide direct evidence that, like HBGAs, bile acid interaction on the capsid is an important cofactor for certain genotypes. However, more unanswered questions seem to arise from these new discoveries. For example, is there an association between the bile acid requirement and the prevalence of certain genotypes? That is, the GII.1 and GII.10 (bile acid binders) genotypes rarely caused outbreaks, whereas the GII.4 and GII.17 genotypes (bile acid nonbinders) were responsible for large epidemics. Therefore, it seems plausible that certain genotypes require bile acids, whereas others have modified their bile acid requirements on the capsid.

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Structural Basis for New Pattern of Conserved Amino Acid Residues Related to Chitin-binding in the Antifungal Peptide from the Coconut Rhinoceros BeetleOryctes rhinoceros

Journal of Biological Chemistry ◽

10.1074/jbc.m301025200 ◽

2003 ◽

Vol 278 (25) ◽

pp. 22820-22827 ◽

Cited By ~ 13

Author(s):

Hikaru Hemmi ◽

Jun Ishibashi ◽

Tetsuya Tomie ◽

Minoru Yamakawa

Keyword(s):

Amino Acid ◽

Structural Basis ◽

Antifungal Peptide ◽

Amino Acid Residues

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The amino acid sequence of the zinc-requiring β-lactamase II from the bacterium Bacillus cereus 569

FEBS Letters ◽

10.1016/0014-5793(85)81024-3 ◽

1985 ◽

Vol 189 (2) ◽

pp. 207-211 ◽

Cited By ~ 16

Author(s):

Richard P. Ambler ◽

Margaret Daniel ◽

Joan Fleming ◽

Jose-Miguel Hermoso ◽

Calvin Pang ◽

...

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Bacillus Cereus ◽

Bacterium Bacillus

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Do antibodies recognize amino acid side chains of protein antigens independently of the carbon backbone?

Journal of Experimental Medicine ◽

10.1084/jem.167.6.1841 ◽

1988 ◽

Vol 167 (6) ◽

pp. 1841-1848 ◽

Cited By ~ 19

Author(s):

V H Van Cleave ◽

C W Naeve ◽

D W Metzger

Keyword(s):

Amino Acid ◽

Peptide Sequence ◽

Structural Basis ◽

Side Chains ◽

Protein Antigens ◽

Carbon Backbone ◽

Internal Image ◽

Amino Acid Side Chains ◽

V Region ◽

Complementarity Determining Region

In an effort to understand the structural basis for antigen mimicry by internal image antibodies, we determined the variable (V) region sequences of two mouse mAbs that mimic the rabbit Ig a1 allotype. The results showed that while the mAb light chains did not contain any allotype-related residues, both heavy chain V regions contained within complementarity-determining region 2 an unusual sequence homologous to the nominal antigen but in opposite orientation with respect to the carbon backbone. The ability of the internal image reversed sequence to express an a1-like determinant was tested directly by producing synthetic peptides that corresponded to the presumed antigenic regions of rabbit Ig and the mAb internal images, respectively. Although the two peptides presented the homologous residues in opposite orientations, they both completely inhibited at similar concentrations the binding of rabbit Ig to anti-a1 antibody. Conservative substitutions in the peptide sequence identified a paired Thr and Glu as being critical for expression of the a1 epitope. These findings indicate that antibodies can recognize the molecular environments created by amino acid side chains independently from the orientation of the protein carbon backbone.

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

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1920097117 ◽

2020 ◽

Vol 117 (20) ◽

pp. 10806-10817 ◽

Cited By ~ 6

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.

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