scholarly journals Clues to reaction specificity in PLP-dependent fold type I enzymes of monosaccharide biosynthesis

2021 ◽  
Author(s):  
Jaya Srivastava ◽  
Petety V. Balaji
Keyword(s):  
Position Weight Matrix ◽  
Catalytic Mechanism ◽  
Sequence Motif ◽  
Type I ◽  
Functional Diversification ◽  
Nucleotide Sugar ◽  
Fold Type ◽  
Reaction Specificity ◽  
Generic Family ◽  
Shed Light

Novel functions can emerge in an enzyme family while conserving catalytic mechanism, motif or fold. PLP-dependent enzymes have evolved into seven fold types and catalyse diverse reactions using the same mechanism for the formation of external aldimine. Nucleotide sugar aminotransferases (NSATs) and dehydratases (NSDs) belong to fold type I and mediate the biosynthesis of several monosaccharides. NSATs use diverse substrates but are highly selective to the C3 or C4 carbon to which amine group is transferred. Factors responsible for reaction specificity in NSDs are known but remain unexplored in NSATs. Profile HMMs were able to identify NSATs but could not capture reaction specificity. A search for discriminating features led to the discovery of a sequence motif that is located near the pyranose binding site suggesting their role in imparting reaction specificity. Using a position weight matrix for this motif, we were able to assign reaction specificity to a large number of NSATs. Residues which upon mutation could convert NSD to NSAT have been reported in literature and we deduced that these are not conserved. This suggested the occurrence of non-generic family specific mutations underlying the evolution of dehydratases. Inferences from this analysis set way for future experiments that can shed light on mechanisms of functional diversification in enzymes of fold type I.

scholarly journals Structural insights into the catalytic mechanism of Bacillus subtilis BacF

2020 ◽  
Vol 76 (3) ◽  
pp. 145-151
Author(s):  
Ashish Deshmukh ◽  
Balasubramanian Gopal
Keyword(s):  
Bacillus Subtilis ◽  
Catalytic Mechanism ◽  
Type I ◽  
Concerted Action ◽  
Substrate Preferences ◽  
Fold Type ◽  
Structural Insights ◽  
Insight Into ◽  
Chemical Analogue

The nonribosomal biosynthesis of the dipeptide antibiotic bacilysin is achieved by the concerted action of multiple enzymes in the Bacillus subtilis bac operon. BacF (YwfG), encoded by the bacF gene, is a fold type I pyridoxal 5-phosphate (PLP)-dependent stereospecific transaminase. Activity assays with L-phenylalanine and 4-hydroxyphenylpyruvic acid (4HPP), a chemical analogue of tetrahydrohydroxyphenylpyruvic acid (H4HPP), revealed stereospecific substrate preferences, a finding that was consistent with previous reports on the role of this enzyme in bacilysin synthesis. The crystal structure of this dimeric enzyme was determined in its apo form as well as in substrate-bound and product-bound conformations. Two ligand-bound structures were determined by soaking BacF crystals with substrates (L-phenylalanine and 4-hydroxyphenylpyruvate). These structures reveal multiple catalytic steps: the internal aldimine with PLP and two external aldimine conformations that show the rearrangement of the external aldimine to generate product (L-tyrosine). Together, these structural snapshots provide an insight into the catalytic mechanism of this transaminase.

scholarly journals The STING1 network regulates autophagy and cell death

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Ruoxi Zhang ◽  
Rui Kang ◽  
Daolin Tang
Keyword(s):  
Cell Death ◽  
Mitotic Cell ◽  
Therapeutic Interventions ◽  
Type I Interferons ◽  
Microbial Pathogens ◽  
Type I ◽  
Autophagic Degradation ◽  
Health And Disease ◽  
Shed Light ◽  
Pro Inflammatory Cytokines

AbstractCell death and immune response are at the core of life. In past decades, the endoplasmic reticulum (ER) protein STING1 (also known as STING or TMEM173) was found to play a fundamental role in the production of type I interferons (IFNs) and pro-inflammatory cytokines in response to DNA derived from invading microbial pathogens or damaged hosts by activating multiple transcription factors. In addition to this well-known function in infection, inflammation, and immunity, emerging evidence suggests that the STING1-dependent signaling network is implicated in health and disease by regulating autophagic degradation or various cell death modalities (e.g., apoptosis, necroptosis, pyroptosis, ferroptosis, mitotic cell death, and immunogenic cell death [ICD]). Here, we outline the latest advances in our understanding of the regulating mechanisms and signaling pathways of STING1 in autophagy and cell death, which may shed light on new targets for therapeutic interventions.

scholarly journals Role of Hypoxia-Mediated Autophagy in Tumor Cell Death and Survival

Cancers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 533
Author(s):  
Rania F. Zaarour ◽  
Bilal Azakir ◽  
Edries Y. Hajam ◽  
Husam Nawafleh ◽  
Nagwa A. Zeinelabdin ◽  
...  
Keyword(s):  
Cell Death ◽  
Type I ◽  
Dependent Manner ◽  
Destruction Process ◽  
Tumor Cell Death ◽  
Complex Regulation ◽  
Cancer Immunotherapies ◽  
The Relationship ◽  
Shed Light

Programmed cell death or type I apoptosis has been extensively studied and its contribution to the pathogenesis of disease is well established. However, autophagy functions together with apoptosis to determine the overall fate of the cell. The cross talk between this active self-destruction process and apoptosis is quite complex and contradictory as well, but it is unquestionably decisive for cell survival or cell death. Autophagy can promote tumor suppression but also tumor growth by inducing cancer-cell development and proliferation. In this review, we will discuss how autophagy reprograms tumor cells in the context of tumor hypoxic stress. We will illustrate how autophagy acts as both a suppressor and a driver of tumorigenesis through tuning survival in a context dependent manner. We also shed light on the relationship between autophagy and immune response in this complex regulation. A better understanding of the autophagy mechanisms and pathways will undoubtedly ameliorate the design of therapeutics aimed at targeting autophagy for future cancer immunotherapies.

scholarly journals A 5′ splice site mutation affecting the pre-mRNA splicing of two upstream exons in the collagen COL1A1 gene. Exon 8 skipping and altered definition of exon 7 generates truncated proα1(I) chains with a non-collagenous insertion destabilizing the triple helix

1994 ◽  
Vol 302 (3) ◽  
pp. 729-735 ◽  
Author(s):  
J F Bateman ◽  
D Chan ◽  
I Moeller ◽  
M Hannagan ◽  
W G Cole
Keyword(s):  
Splice Site ◽  
De Novo ◽  
Donor Site ◽  
Mrna Splicing ◽  
Splice Donor Site ◽  
Sequence Motif ◽  
Type I ◽  
Splice Donor ◽  
Site Mutation ◽  
Definition Of

A heterozygous de novo G to A point mutation in intron 8 at the +5 position of the splice donor site of the gene for the pro alpha 1(I) chain of type I procollagen, COL1A1, was defined in a patient with type IV osteogenesis imperfecta. The splice donor site mutation resulted not only in the skipping of the upstream exon 8 but also unexpectedly had the secondary effect of activating a cryptic splice site in the next upstream intron, intron 7, leading to re-definition of the 3′ limit of exon 7. These pre-mRNA splicing aberrations cause the deletion of exon 8 sequences from the mature mRNA and the inclusion of 96 bp of intron 7 sequence. Since the mis-splicing of the mutant allele product resulted in the maintenance of the correct codon reading frame, the resultant pro alpha 1(I) chain contained a short non-collagenous 32-amino-acid sequence insertion within the repetitive Gly-Xaa-Yaa collagen sequence motif. At the protein level, the mutant alpha 1(I) chain was revealed by digestion with pepsin, which cleaved the mutant procollagen within the protease-sensitive non-collagenous insertion, producing a truncated alpha 1(I). This protease sensitivity demonstrated the structural distortion to the helical structure caused by the insertion. In long-term culture with ascorbic acid, which stimulates the formation of a mature crosslinked collagen matrix, and in tissues, there was no evidence of the mutant chain, suggesting that during matrix formation the mutant chain was unable to stably incorporated into the matrix and was degraded proteolytically.

Activities of Arabidopsis sinapoylglucose:malate sinapoyltransferase shed light on functional diversification of serine carboxypeptidase-like acyltransferases

2008 ◽  
Vol 69 (9) ◽  
pp. 1826-1831 ◽  
Author(s):  
Felix Stehle ◽  
Wolfgang Brandt ◽  
Jürgen Schmidt ◽  
Carsten Milkowski ◽  
Dieter Strack
Keyword(s):  
Serine Carboxypeptidase ◽  
Functional Diversification ◽  
Shed Light

scholarly journals Metagenomic discovery of CRISPR-associated transposons

2021 ◽  
Vol 118 (49) ◽  
pp. e2112279118
Author(s):  
James R. Rybarski ◽  
Kuang Hu ◽  
Alexis M. Hill ◽  
Claus O. Wilke ◽  
Ilya J. Finkelstein
Keyword(s):  
Gene Editing ◽  
Type I ◽  
Genomic Databases ◽  
Type Iv ◽  
Shed Light

CRISPR-associated Tn7 transposons (CASTs) co-opt cas genes for RNA-guided transposition. CASTs are exceedingly rare in genomic databases; recent surveys have reported Tn7-like transposons that co-opt Type I-F, I-B, and V-K CRISPR effectors. Here, we expand the diversity of reported CAST systems via a bioinformatic search of metagenomic databases. We discover architectures for all known CASTs, including arrangements of the Cascade effectors, target homing modalities, and minimal V-K systems. We also describe families of CASTs that have co-opted the Type I-C and Type IV CRISPR-Cas systems. Our search for non-Tn7 CASTs identifies putative candidates that include a nuclease dead Cas12. These systems shed light on how CRISPR systems have coevolved with transposases and expand the programmable gene-editing toolkit.

scholarly journals Comparison of human poly-N-acetyl-lactosamine synthase structure with GT-A fold glycosyltransferases supports a modular assembly of catalytic subsites

2020 ◽  
pp. jbc.RA120.015305
Author(s):  
Renuka Kadirvelraj ◽  
Jeong-Yeh Yang ◽  
Hyun Woo Kim ◽  
Justin H. Sanders ◽  
Kelley W. Moremen ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Binding Site ◽  
Human Disease ◽  
Catalytic Mechanism ◽  
Substrate Recognition ◽  
Nucleotide Sugar ◽  
Modular Assembly ◽  
Acceptor Specificity ◽  
Donor Acceptor ◽  
Prior Models

Poly-N-acetyl-lactosamine (poly-LacNAc) structures are composed of repeating [-Galβ(1,4)-GlcNAcβ(1,3)-]n glycan extensions. They are found on both N- and O­-glycoproteins and glycolipids, and play an important role in development, immune function, and human disease. The majority of mammalian poly-LacNAc is synthesized by the alternating iterative action of β1,3-N-acetylglucosaminyltransferase 2 (B3GNT2) and β1,4-galactosyltransferases. B3GNT2 is in the largest mammalian glycosyltransferase family, GT31, but little is known about the structure, substrate recognition, or catalysis by family members. Here we report the structures of human B3GNT2 in complex with UDP:Mg2+, and in complex with both UDP:Mg2+ and a glycan acceptor, lacto-N-neotetraose. The B3GNT2 structure conserves the GT-A fold and the DxD motif that coordinates a Mg2+ ion for binding the UDP-GlcNAc sugar donor. The acceptor complex shows interactions with only the terminal Galβ(1,4)-GlcNAcβ(1,3)- disaccharide unit, which likely explains the specificity for both N- and O-glycan acceptors. Modeling of the UDP-GlcNAc donor supports a direct displacement inverting catalytic mechanism. Comparative structural analysis indicates that nucleotide sugar donors for GT-A fold glycosyltransferases bind in similar positions and conformations without conserving interacting residues, even for enzymes that use the same donor substrate. In contrast, the B3GNT2 acceptor binding site is consistent with prior models suggesting that the evolution of acceptor specificity involves loops inserted into the stable GT-A fold. These observations support the hypothesis that GT-A fold glycosyltransferases employ co-evolving donor, acceptor, and catalytic subsite modules as templates to achieve the complex diversity of glycan linkages in biological systems.

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