6,826 results match your criteria superfamily conserved


Adaptive evolution of Moniliophthora PR-1 proteins towards its pathogenic lifestyle.

BMC Ecol Evol 2021 May 14;21(1):84. Epub 2021 May 14.

Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.

Background: Plant pathogenesis related-1 (PR-1) proteins belong to the CAP superfamily and have been characterized as markers of induced defense against pathogens. Moniliophthora perniciosa and Moniliophthora roreri are hemibiotrophic fungi that respectively cause the witches' broom disease and frosty pod rot in Theobroma cacao. Interestingly, a large number of plant PR-1-like genes are present in the genomes of both species and many are up-regulated during the biotrophic interaction. Read More

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The large extracellular loop of CD63 interacts with gp41 of HIV-1 and is essential for establishing the virological synapse.

Sci Rep 2021 May 11;11(1):10011. Epub 2021 May 11.

HIV and Other Retroviruses, Robert Koch Institute, Nordufer 20, 13353, Berlin, Germany.

Human immunodeficiency virus type 1 (HIV-1) persists lifelong in infected individuals and has evolved unique strategies in order to evade the immune system. One of these strategies is the direct cell-to-cell spread of HIV-1. The formation of a virological synapse (VS) between donor and target cell is important for this process. Read More

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Distribution of Merlin in eukaryotes and first report of DNA transposons in kinetoplastid protists.

PLoS One 2021 6;16(5):e0251133. Epub 2021 May 6.

Laboratório de Ciências e Tecnologias Aplicadas em Saúde (LaCTAS), Instituto Carlos Chagas, Fundação Oswaldo Cruz (Fiocruz), Curitiba, PR, Brazil.

DNA transposons are defined as repeated DNA sequences that can move within the host genome through the action of transposases. The transposon superfamily Merlin was originally found mainly in animal genomes. Here, we describe a global distribution of the Merlin in animals, fungi, plants and protists, reporting for the first time their presence in Rhodophyceae, Metamonada, Discoba and Alveolata. Read More

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-regulatory elements in conserved non-coding sequences of nuclear receptor genes indicate for crosstalk between endocrine systems.

Open Med (Wars) 2021 12;16(1):640-650. Epub 2021 Apr 12.

Sahlgrenska University Hospital, Gothia Forum for Clinical Research, Gothenburg, Sweden.

Nuclear receptors (NRs) are ligand-activated transcription factors that regulate gene expression when bound to specific DNA sequences. Crosstalk between steroid NR systems has been studied for understanding the development of hormone-driven cancers but not to an extent at a genetic level. This study aimed to investigate crosstalk between steroid NRs in conserved intron and exon sequences, with a focus on steroid NRs involved in prostate cancer etiology. Read More

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Genome-wide investigation of the AP2/ERF superfamily and their expression under salt stress in Chinese willow ().

PeerJ 2021 13;9:e11076. Epub 2021 Apr 13.

Lab of Landscape Plant Genetics and Breeding, School of Life Science, Nantong University, Nantong, Jiangsu, China.

AP2/ERF transcription factors (TFs) play indispensable roles in plant growth, development, and especially in various abiotic stresses responses. The AP2/ERF TF family has been discovered and classified in more than 50 species. However, little is known about the gene family of Chinese willow (), which is a tetraploid ornamental tree species that is widely planted and is also considered as a species that can improve the soil salinity of coastal beaches. Read More

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Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of a d-Amino Acid.

Biochemistry 2021 May 5. Epub 2021 May 5.

Department of Genetics, University of Georgia, Athens, Georgia 30602, United States.

d-Glucosaminate-6-phosphate ammonia-lyase (DGL) is a pyridoxal 5'-phosphate (PLP)-dependent enzyme that produces 2-keto-3-deoxygluconate 6-phosphate (KDG-6-P) in the metabolism of d-glucosaminic acid by serovar typhimurium. We have determined the crystal structure of DGL by SAD phasing with selenomethionine to a resolution of 2.58 Å. Read More

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Carbapenem-resistance determinants acquired through novel chromosomal integrations in XDR .

Antimicrob Agents Chemother 2021 May 3. Epub 2021 May 3.

Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway

Two novel or containing genomic islands (GIs) were discovered in four extensively drug-resistant (XDR) isolated from in-patients at a tertiary hospital in Ghana by whole-genome sequence analyses. The strains were of ST234 and formed a phylogenetic clade together with ST111, recognized as a global high-risk clone. Their carbapenem resistance was encoded by Tn-type integrons, In1592 () and In1595 (), both carrying complete mobilization modules. Read More

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Genome-wide characterization and expression and co-expression analysis suggested diverse functions of genes in bread wheat.

Heliyon 2020 Dec 29;6(12):e05762. Epub 2020 Dec 29.

Department of Botany, Panjab University, Chandigarh, 160014, India.

WUSCHEL-related homeobox () genes belong to the homeobox superfamily, are plant-specific and play vital functions in the growth and development. Herein, we identified a total of 43 genes in the allohexaploid (AABBDD) genome of L These genes were distributed on the various chromosomes of each subgenome (A, B and D). The phylogenetic analysis showed the clustering of TaWOXs into three clades: ancient, intermediate and modern or WUS. Read More

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December 2020

The SpeG Spermidine/Spermine -Acetyltransferase Allosteric Loop and β6-β7 Structural Elements Are Critical for Kinetic Activity.

Front Mol Biosci 2021 13;8:645768. Epub 2021 Apr 13.

Department of Chemistry & Biochemistry, San Francisco State University, San Francisco, CA, United States.

Polyamines regulate many important biological processes including gene expression, intracellular signaling, and biofilm formation. Their intracellular concentrations are tightly regulated by polyamine transport systems and biosynthetic and catabolic pathways. Spermidine/spermine -acetyltransferases (SSATs) are catabolic enzymes that acetylate polyamines and are critical for maintaining intracellular polyamine homeostasis. Read More

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Genome-Wide Analysis of the Late Embryogenesis Abundant (LEA) and Abscisic Acid-, Stress-, and Ripening-Induced (ASR) Gene Superfamily from and Their Roles in Salinity/Alkaline and Drought Tolerance.

Int J Mol Sci 2021 Apr 27;22(9). Epub 2021 Apr 27.

Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.

(bay bean), distributing in coastal areas or islands in tropical and subtropical regions, is an extremophile halophyte with good adaptability to seawater and drought. Late embryogenesis abundant (LEA) proteins typically accumulate in response to various abiotic stresses, including dehydration, salinity, high temperature, and cold, or during the late stage of seed development. Abscisic acid-, stress-, and ripening-induced (ASR) genes are stress and developmentally regulated plant-specific genes. Read More

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Conserved Conformational Hierarchy across Functionally Divergent Glycosyltransferases of the GT-B Structural Superfamily as Determined from Microsecond Molecular Dynamics.

Int J Mol Sci 2021 Apr 28;22(9). Epub 2021 Apr 28.

Bioinformatics and Computational Biology Program, University of Minnesota, Minneapolis, MN 55455, USA.

It has long been understood that some proteins undergo conformational transitions en route to the Michaelis Complex to allow chemistry. Examination of crystal structures of glycosyltransferase enzymes in the GT-B structural class reveals that the presence of ligand in the active site triggers an open-to-closed conformation transition, necessary for their catalytic functions. Herein, we describe microsecond molecular dynamics simulations of two distantly related glycosyltransferases that are part of the GT-B structural superfamily, HepI and GtfA. Read More

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Genome-Wide Identification and Characterization of TALE Superfamily Genes in Soybean ( L.).

Int J Mol Sci 2021 Apr 16;22(8). Epub 2021 Apr 16.

Soybean Research Institute, National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Collaborative Innovation Center for Modern Crop Production, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.

The three-amino-acid-loop-extension (TALE) superfamily genes broadly existed in plants, which played important roles in plant growth, development and abiotic stress responses. In this study, we identified 68 TALE (GmTALE) superfamily members. Phylogenetic analysis divided the GmTALE superfamily into the BEL1-like (BLH/BELL homeodomain) and the KNOX (KNOTTED-like homeodomain) subfamilies. Read More

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Genome-Wide Analysis of the RAV Transcription Factor Genes in Rice Reveals Their Response Patterns to Hormones and Virus Infection.

Viruses 2021 Apr 25;13(5). Epub 2021 Apr 25.

State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Key Laboratory of Biotechnology in Plant Protection of Ministry of Agriculture and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.

The RAV family is part of the B3 superfamily and is one of the most abundant transcription factor families in plants. Members have highly conserved B3 or AP2 DNA binding domains. Although the family genes of several species have been systematically identified from genome-wide studies, there has been no comprehensive study to identify rice family genes. Read More

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Death domain fold proteins in immune signaling and transcriptional regulation.

Authors:
Yu-San Huoh Sun Hur

FEBS J 2021 Apr 27. Epub 2021 Apr 27.

Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute at Harvard Medical School, Boston, MA, USA.

Death domain fold (DDF) superfamily comprises of the death domain (DD), death effector domain (DED), caspase activation recruitment domain (CARD), and pyrin domain (PYD). By utilizing a conserved mode of interaction involving six distinct surfaces, a DDF serves as a building block that can densely pack into homomultimers or filaments. Studies of immune signaling components have revealed that DDF-mediated filament formation plays a central role in mediating signal transduction and amplification. Read More

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Mitogenome of emAlaudala/em emcheleensis/em (Passeriformes: Alaudidae) and comparative analyses of Sylvioidea mitogenomes.

Zootaxa 2021 Apr 9;4952(2):zootaxa.4952.2.7. Epub 2021 Apr 9.

College of Life Sciences, Shaanxi Normal University, Xi'an 710062, China Shaanxi Institute of Zoology, Xi'an 710032, China.

To gain a better understanding of mitogenome features and phylogenetic relationships in Sylvioidea, a superfamily of Passerida, suborder Passeri, Passeriformes, the whole mitogenome of Alaudala cheleensis Swinhoe (Alaudidae) was sequenced, a comparative mitogenomic analysis of 18 Sylvioidea species was carried out, and finally, a phylogeny was reconstructed based on the mitochondrial dataset. Gene order of the A. cheleensis mitogenome was similar to that of other Sylvioidea species, including the gene rearrangement of cytb-trnT-CR1-trnP-nad6-trnE-remnant CR2-trnF-rrnS. Read More

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A conserved residue in the P2X4 receptor has a non-conserved function in ATP recognition.

J Biol Chem 2021 Apr 23:100655. Epub 2021 Apr 23.

School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China;. Electronic address:

Highly conserved amino acids are generally anticipated to have similar functions across a protein superfamily, including that of the P2X ion channels, which are gated by extracellular ATP. However, whether and how these functions are conserved becomes less clear when neighboring amino acids are not conserved. Here, we investigate one such case, focused on the highly conserved residue from P2X4, E118 (rat P2X4 numbering, rP2X4), a P2X subtype associated with human neuropathic pain. Read More

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Biosynthesis of d--l--Heptose in the Capsular Polysaccharides of .

Biochemistry 2021 Apr 26. Epub 2021 Apr 26.

Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas 77843, United States.

is the leading cause of food poisoning in the United States and Europe. The exterior cell surface of is coated with a capsular polysaccharide (CPS) that is essential for the maintenance and integrity of the bacterial cell wall and evasion of the host immune response. The identity and sequences of the monosaccharide components of the CPS are quite variable and dependent on the specific strain of . Read More

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Mitochondrial analysis of oribatid mites provides insights into their atypical tRNA annotation, genome rearrangement and evolution.

Parasit Vectors 2021 Apr 23;14(1):221. Epub 2021 Apr 23.

Department of Health Inspection and Quarantine, Wannan Medical College, Wuhu, Anhui Province, 241002, People's Republic of China.

Background: The mitochondrial (mt) genomes of Sarcoptiformes mites typically contain 37 genes. Although the loss of genes is rare in Sarcoptiformes mite mitogenomes, two of the six previously reported oribatid mites (Acariforms: Sarcoptiformes) are reported to have lost parts of their tRNA genes. To confirm whether the tRNA genes were indeed lost and whether the loss is universal, we re-annotated the available oribatid mite sequences and sequenced the mitogenome of Oribatula sakamorii. Read More

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Ly-6D of Japanese flounder (Paralichthys olivaceus) functions as a complement regulator and promotes host clearance of pathogen.

Dev Comp Immunol 2021 Apr 20;122:104104. Epub 2021 Apr 20.

Institute of Tropical Bioscience and Biotechnology, Hainan Academy of Tropical Agricultural Resource, CATAS, Haikou, 571101, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Hainan Provincial Key Laboratory for Functional Components Research and Utilization of Marine Bio-resources, Haikou, 571101, China. Electronic address:

The Lymphocyte antigen-6 (Ly-6) superfamily has been considered to play an important role in the innate immunity of mammals. The functions of Ly-6 proteins are diverse since their low sequence homology. Currently, the function of Ly-6D, a member of Ly-6 family proteins, is completely unknown in teleost. Read More

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Molecular characterization and enzyme inhibition studies of NADP+- farnesol dehydrogenase from diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae).

Biosci Biotechnol Biochem 2021 Apr 23. Epub 2021 Apr 23.

Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), 43600 UKM, Bangi, Selangor, Malaysia.

Juvenile hormone III (JH III) plays an important role in insect reproduction, development, and behavior. The second branch of JH III production includes oxidation of farnesol to farnesal by farnesol dehydrogenase. This study reported the identification and characterization of Plutella xylostella farnesol dehydrogenase (PxFoLDH). Read More

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Assessment of Babesia bovis 6cys A and 6cys B as components of transmission blocking vaccines for babesiosis.

Parasit Vectors 2021 Apr 20;14(1):210. Epub 2021 Apr 20.

Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA, USA.

Background: Babesia bovis reproduces sexually in the gut of its tick vector Rhipicephalus microplus, which involves expression of 6cys A and 6cys B proteins. Members of the widely conserved 6cys superfamily are candidates for transmission blocking vaccines (TBV), but intricacies in the immunogenicity of the 6cys proteins in the related Plasmodium parasites required the identification of transmission blocking domains in these molecules for vaccine design. Hereby, the immunogenic efficacy of recombinant (r) B. Read More

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Characterization of tolloid-mediated cleavage of the GDF8 procomplex.

Biochem J 2021 May;478(9):1733-1747

Department of Molecular Genetics, Biochemistry, and Microbiology, University of Cincinnati, College of Medicine, Cincinnati, OH 45267, U.S.A.

Growth differentiation factor 8 (GDF8), a.k.a. Read More

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Transforming growth factor beta signaling: The master sculptor of fingers.

Dev Dyn 2021 Apr 19. Epub 2021 Apr 19.

Departamento de Anatomía y Biología Celular and IDIVAL, Universidad de Cantabria, Santander, Spain.

Transforming growth factor beta (TGFβ) constitutes a large and evolutionarily conserved superfamily of secreted factors that play essential roles in embryonic development, cancer, tissue regeneration, and human degenerative pathology. Studies of this signaling cascade in the regulation of cellular and tissue changes in the three-dimensional context of a developing embryo have notably advanced in the understanding of the action mechanism of these growth factors. In this review, we address the role of TGFβ signaling in the developing limb, focusing on its essential function in the morphogenesis of the autopod. Read More

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Molecular Mechanism of Nramp-Family Transition Metal Transport.

J Mol Biol 2021 Apr 16:166991. Epub 2021 Apr 16.

Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

The Natural resistance-associated macrophage protein (Nramp) family of transition metal transporters enables uptake and trafficking of essential micronutrients that all organisms must acquire to survive. Two decades after Nramps were identified as proton-driven, voltage-dependent secondary transporters, multiple Nramp crystal structures have begun to illustrate the fine details of the transport process and provide a new framework for understanding a wealth of preexisting biochemical data. Here we review the relevant literature pertaining to Nramps' biological roles and especially their conserved molecular mechanism, including our updated understanding of conformational change, metal binding and transport, substrate selectivity, proton transport, proton-metal coupling, and voltage dependence. Read More

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A novel predicted ADP-ribosyltransferase-like family conserved in eukaryotic evolution.

PeerJ 2021 10;9:e11051. Epub 2021 Mar 10.

Department of Biochemistry and Microbiology, Warsaw University of Life Sciences - SGGW, Warszawa, Poland.

The presence of many completely uncharacterized proteins, even in well-studied organisms such as humans, seriously hampers full understanding of the functioning of the living cells. ADP-ribosylation is a common post-translational modification of proteins; also nucleic acids and small molecules can be modified by the covalent attachment of ADP-ribose. This modification, important in cellular signalling and infection processes, is usually executed by enzymes from the large superfamily of ADP-ribosyltransferases (ARTs). Read More

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Evolutionary research on the expansin protein family during the plant transition to land provides new insights into the development of Tartary buckwheat fruit.

BMC Genomics 2021 Apr 9;22(1):252. Epub 2021 Apr 9.

College of Life Science, Sichuan Agricultural University, Ya'an, 625014, China.

Background: Plant transitions to land require robust cell walls for regulatory adaptations and to resist changing environments. Cell walls provide essential plasticity for plant cell division and defense, which are often conferred by the expansin superfamily with cell wall-loosening functions. However, the evolutionary mechanisms of expansin during plant terrestrialization are unclear. Read More

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Molecular modeling and molecular dynamics simulation studies on thyroid hormone receptor from Rattus norvegicus: role of conserved water molecules.

J Mol Model 2021 Apr 8;27(5):126. Epub 2021 Apr 8.

Department of Chemistry, National Institute of Technology-Durgapur, Durgapur, West Bengal, 713209, India.

Thyroid hormone receptor (THR) belongs to the nuclear receptor (NR) superfamily that is activated by binding of appropriate ligand molecules (thyroid hormones). These receptors directly bind to specific DNA sequences for gene expression, which is essential for metabolism, homeostasis, and the development of organisms, making it an important drug target. Extensive MD-simulation studies of triiodothyronine (T3) docked modeled rnTHRβ1 structures have indicated the presence of twelve conserved water molecules at the DNA-DBD (DNA binding domain) interface. Read More

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PLD3 is a neuronal lysosomal phospholipase D associated with β-amyloid plaques and cognitive function in Alzheimer's disease.

PLoS Genet 2021 Apr 8;17(4):e1009406. Epub 2021 Apr 8.

Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America.

Phospholipase D3 (PLD3) is a protein of unclear function that structurally resembles other members of the phospholipase D superfamily. A coding variant in this gene confers increased risk for the development of Alzheimer's disease (AD), although the magnitude of this effect has been controversial. Because of the potential significance of this obscure protein, we undertook a study to observe its distribution in normal human brain and AD-affected brain, determine whether PLD3 is relevant to memory and cognition in sporadic AD, and to evaluate its molecular function. Read More

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A Superfamily-wide Activity Atlas of Serine Hydrolases in .

Biochemistry 2021 Apr 7;60(16):1312-1324. Epub 2021 Apr 7.

Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra, India 411008.

The serine hydrolase (SH) superfamily is, perhaps, one of the largest functional enzyme classes in all forms of life and consists of proteases, peptidases, lipases, and carboxylesterases as representative members. Consistent with the name of this superfamily, all members, without any exception to date, use a nucleophilic serine residue in the enzyme active site to perform hydrolytic-type reactions via a two-step ping-pong mechanism involving a covalent enzyme intermediate. Given the highly conserved catalytic mechanism, this superfamily has served as a classical prototype in the development of several platforms of chemical proteomics techniques, activity-based protein profiling (ABPP), to globally interrogate the functions of its different members in various native, yet complex, biological settings. Read More

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Criticality of a conserved tyrosine residue in the SpeG protein from Escherichia coli.

Protein Sci 2021 Apr 7. Epub 2021 Apr 7.

Department of Chemistry and Biochemistry, San Francisco State University, San Francisco, California, USA.

The SpeG spermidine/spermine N-acetyltransferase (SSAT) from Escherichia coli belongs to the Gcn5-related N-acetyltransferase (GNAT) superfamily of proteins. In vitro characterization of this enzyme shows it acetylates the polyamines spermine and spermidine, with a preference toward spermine. This enzyme has a conserved tyrosine residue (Y135) that is found in all SSAT proteins and many GNAT functional subfamilies. Read More

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