• Genomics & Informatics
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• v.7 no.2
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• pp.131-135
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• 2009

Domains are the building blocks of proteins. Exon shuffling is an important mechanism accounting for combination of a limited repertoire of protein domains in the evolution of multicellular species. A relative excess of domains encoded by symmetric exons in metazoan phyla has been presented as evidence of exon shuffling, and symmetric domains can be divided into old and new domains by determining the ages of the domains. In this report, we compare the spread, versatility, and subcellular localization of old and new domains by analyzing eight metazoan genomes and their respective annotated proteomes. We found that new domains have been expanding as multicellular organisms evolved, and this expansion was principally because of increases in class 1-1 domains amongst several classes of domain families. We also found that younger domains have been expanding in membranes and secreted proteins along with multi-cellular organism evolution. In contrast, old domains are located mainly in nuclear and cytoplasmic proteins. We conclude that the increasing mobility and versatility of new domains, in contrast to old domains, plays a significant role in metazoan evolution, facilitating the creation of secreted and transmembrane multidomain proteins unique to metazoa.

• Molecules and Cells
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• v.43 no.3
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• pp.286-297
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• 2020

Mammalian patatin-like phospholipase domain containing proteins (PNPLAs) play critical roles in triglyceride hydrolysis, phospholipids metabolism, and lipid droplet (LD) homeostasis. PNPLA7 is a lysophosphatidylcholine hydrolase anchored on the endoplasmic reticulum which associates with LDs through its catalytic region (PNPLA7-C) in response to increased cyclic nucleotide levels. However, the interaction of PNPLA7 with LDs through its catalytic region is unknown. Herein, we demonstrate that PNPLA7-C localizes to the mature LDs ex vivo and also colocalizes with pre-existing LDs. Localization of PNPLA7-C with LDs induces LDs clustering via non-enzymatic intermolecular associations, while PNPLA7 alone does not induce LD clustering. Residues 742-1016 contains four putative transmembrane domains which act as a LD targeting motif and are required for the localization of PNPLA7-C to LDs. Furthermore, the N-terminal flanking region of the LD targeting motif, residues 681-741, contributes to the LD targeting, whereas the C-terminal flanking region (1169-1326) has an anti-LD targeting effect. Interestingly, the LD targeting motif does not exhibit lysophosphatidylcholine hydrolase activity even though it associates with LDs phospholipid membranes. These findings characterize the specific functional domains of PNPLA7 mediating subcellular positioning and interactions with LDs, as wells as providing critical insights into the structure of this evolutionarily conserved phospholipid-metabolizing enzyme family.

• Journal of Applied Biological Chemistry
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• v.48 no.3
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• pp.127-132
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• 2005

MYB genes, comprising group of related genes found in animal, plant, and fungal genomes, encode common DNA-binding domains composed of one to four repeat motifs. MYB genes containing two repeats (R2R3) constitute largest MYB gene family in plants. R2R3 MYB genes play important roles in regulation of secondary metabolism, control of cell shape, disease resistance, and hormone response. Eight-four R2R3 MYB genes were retrieved from rice genome for functional characterization of MYB genes. Analysis of MYB domains revealed each MYB domain contains three ${\alpha}$-helices with regularly spaced tryptophan residues. R2R3 MYB genes were divided into four subfamilies based on phylogenic analysis result. Real-time PCR analysis of 34 MYB genes revealed 12 MYB genes were highly expressed in seeds than in leaves, whereas 4 genes were highly expressed in leaves.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1120-1126
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• 2013

The syndecan family consists of four transmembrane heparan sulfate proteoglycans present in most cell types and each syndecan shares a common structure containing a heparan sulfate modified extracellular domain, a single transmembrane domain and a C-terminal cytoplasmic domain. To get a better understanding of the mechanism and function of syndecan-4 which is one of the syndecan family, it is crucial to investigate its three-dimensional structure. Unfortunately, it is difficult to prepare the peptide because it is membrane-bound protein that transverses the lipid bilayer of the cell membrane. Here, we optimize the expression, purification, and characterization of transmembrane, cytoplasmic and short extracellular domains of syndecan4 (syndecan-4 eTC). Syndecan-4 eTC was successfully obtained with high purity and yield from the M9 medium. The structural information of syndecan-4 eTC was investigated by MALDI-TOF mass (MS) spectrometry, circular dichroism (CD) spectroscopy, and nuclear magnetic resonance (NMR) spectroscopy. It was confirmed that syndecan-4 eTC had an ${\alpha}$-helical multimeric structure like transmembrane domain of syndecan-4 (syndecan-4 TM) in membrane environments.

• Journal of Microbiology and Biotechnology
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• v.28 no.4
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• pp.597-605
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• 2018

Acyl-CoA oxidases (ACOXs) play important roles in lipid metabolism, including peroxisomal fatty acid ${\beta}$-oxidation by the conversion of acyl-CoAs to 2-trans-enoyl-CoAs. The yeast Yarrowia lipolytica can utilize fatty acids as a carbon source and thus has extensive biotechnological applications. The crystal structure of ACOX3 from Y. lipolytica (YlACOX3) was determined at a resolution of $2.5{\AA}$. It contained two molecules per asymmetric unit, and the monomeric structure was folded into four domains; $N{\alpha}$, $N{\beta}$, $C{\alpha}1$, and $C{\alpha}2$ domains. The cofactor flavin adenine dinucleotide was bound in the dimer interface. The substrate-binding pocket was located near the cofactor, and formed at the interface between the $N{\alpha}$, $N{\beta}$, and $C{\alpha}1$ domains. Comparisons with other ACOX structures provided structural insights into how YlACOX has a substrate preference for short-chain acyl-CoA. In addition, the structure of YlACOX3 was compared with those of medium- and long-chain ACOXs, and the structural basis for their differences in substrate specificity was discussed.

• Journal of Microbiology and Biotechnology
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• v.31 no.10
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• pp.1393-1400
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• 2021

Acetone-butanol-ethanol (ABE) fermentation by the anaerobic bacterium Clostridium acetobutylicum has been considered a promising process of industrial biofuel production. Phosphotransbutyrylase (phosphate butyryltransferase, PTB) plays a crucial role in butyrate metabolism by catalyzing the reversible conversion of butyryl-CoA into butyryl phosphate. Here, we report the crystal structure of PTB from the Clostridial host for ABE fermentation, C. acetobutylicum, (CaPTB) at a 2.9 Å resolution. The overall structure of the CaPTB monomer is quite similar to those of other acyltransferases, with some regional structural differences. The monomeric structure of CaPTB consists of two distinct domains, the N- and C-terminal domains. The active site cleft was formed at the interface between the two domains. Interestingly, the crystal structure of CaPTB contained eight molecules per asymmetric unit, forming an octamer, and the size-exclusion chromatography experiment also suggested that the enzyme exists as an octamer in solution. The structural analysis of CaPTB identifies the substrate binding mode of the enzyme and comparisons with other acyltransferase structures lead us to speculate that the enzyme undergoes a conformational change upon binding of its substrate.

• Genomics & Informatics
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• v.4 no.3
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• pp.125-128
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• 2006

We present an openfree hypertext (also known as wiki) web cluster called BioCC. BioCC is a novel wiki farm that lets researchers create hundreds of biological web sites. The web sites form an organic information network. The contents of all the sites on the BioCC wiki farm are modifiable by anonymous as well as registered users. This enables biologists with diverse backgrounds to form their own Internet bio-communities. Each community can have custom-made layouts for information, discussion, and knowledge exchange. BioCC aims to form an ever-expanding network of openfree biological knowledge databases used and maintained by biological experts, students, and general users. The philosophy behind BioCC is that the formation of biological knowledge is best achieved by open-minded individuals freely exchanging information. In the near future, the amount of genomic information will have flooded society. BioGG can be an effective and quickly updated knowledge database system. BioCC uses an opensource wiki system called Mediawiki. However, for easier editing, a modified version of Mediawiki, called Biowiki, has been applied. Unlike Mediawiki, Biowiki uses a WYSIWYG (What You See Is What You Get) text editor. BioCC is under a share-alike license called BioLicense (http://biolicense.org). The BioCC top level site is found at http://bio.cc/

• Bulletin of the Korean Chemical Society
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• v.28 no.9
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• pp.1455-1456
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• 2007

• Agricultural and Biosystems Engineering
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• v.2 no.1
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• pp.15-23
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• 2001

On the assumption that the voices of the cows are produced by the linear prediction filter, we characterized the cows’voices. The order of this filter was determined by examining the voice characteristics both in time and frequency domains. The proposed order of the linear prediction filter is 15 for modeling voice production of the cow. The characteristics of the amplitude envelope of the voice signal was investigated by analyzing the sequence of the short time variance both in time and frequency domains, and the new parameters were defined. One of the coefficients o the linear prediction filter generating the voice signal, the fundamental frequency, the slope of the straight line regressed from the log-log spectra of the short time variance and the coefficients of the linear prediction filter generating the sequence of the short time variance of the voice signal can differentiate the two cows.

• Proceedings of the Botanical Society of Korea Conference
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• 2002.04a
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• pp.106-106
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• 2002