• Molecules and Cells
• /
• v.37 no.4
• /
• pp.322-329
• /
• 2014

N-acetylglucosamine kinase (GlcNAc kinase or NAGK; EC 2.7.1.59) is highly expressed and plays a critical role in the development of dendrites in brain neurons. In this study, the authors conducted structure-function analysis to verify the previously proposed 3D model structure of GlcNAc/ATP-bound NAGK. Three point NAGK mutants with different substrate binding capacities and reaction velocities were produced. Wild-type (WT) NAGK showed strong substrate preference for GlcNAc. Conversion of Cys143, which does not make direct hydrogen bonds with GlcNAc, to Ser (i.e., C143S) had the least affect on the enzymatic activity of NAGK. Conversion of Asn36, which plays a role in domain closure by making a hydrogen bond with GlcNAc, to Ala (i.e., N36A) mildly reduced NAGK enzyme activity. Conversion of Asp107, which makes hydrogen bonds with GlcNAc and would act as a proton acceptor during nucleophilic attack on the ${\gamma}$-phosphate of ATP, to Ala (i.e., D107A), caused a total loss in enzyme activity. The overexpression of EGFP-tagged WT or any of the mutant NAGKs in rat hippocampal neurons (DIV 5-9) increased dendritic architectural complexity. Finally, the overexpression of the small, but not of the large, domain of NAGK resulted in dendrite degeneration. Our data show the effect of structure on the functional aspects of NAGK, and in particular, that the small domain of NAGK, and not its NAGK kinase activity, plays a critical role in the upregulation of dendritogenesis.

• Journal of Life Science
• /
• v.16 no.3 s.76
• /
• pp.409-414
• /
• 2006

Molecular chaperones and folding enzymes in the endoplasmic reticulum (ER) associate with the newly synthesized proteins to prevent their aggregation and help them fold and assemble correctly. Chaperone function of BiP, which is a Hsp70 homologue in ER, is controlled by the N-terminal ATPase domain. The ATPase activity of the ATPase domain is affected by regulatory factors. BAP was identified as a nucleotide exchange factor of BiP (Grp78), which exchanges ADP with ATP in the ATPase domain of BiP This study presents whether BAP can influence folding of a protein, immunoglobulin heavy chain that is bound to BiP tightly. We first examined which nucleotide of ADP and ATP affects on BAP binding to BiP The data showed that endogenous BAP of HEK293 cells prefers ADP for binding to BiP in vitro, suggesting that BAP first releases ADP from the ATPase domain in order to exchange with ATP. Immunoglobulin heavy chain, an unfolded protein substrate, was released from BiP in the presence of BAP but not in the presence of ERdj3, which is another regulatory factor for BiP accelerating the rate of ATP hydrolysis of BiP The ADP-releasing function of BAP was, therefore, believed to be responsible for immunoglobulin heavy chain release from BiP. Grp170, another Hsp70 homologue in ER, did not co-precipited with BAP from $[^{35}S]$-metabolic labeled HEK293 lysate containing both overexpressed Grp170 and BAP. These data suggested that BAP has no specificity to Grp170 although the ATPase domains of Grp170 and BiP are homologous each other.

• Journal of Microbiology and Biotechnology
• /
• v.28 no.12
• /
• pp.2036-2045
• /
• 2018

An endo-${\beta}$-1,4-glucanase gene, cel5L, was cloned using the shot-gun method from Bacillus sp.. The gene, which contained a predicted signal peptide, encoded a protein of 496 amino acid residues, and the molecular mass of the mature Cel5L was estimated to be 51.8 kDa. Cel5L contained a catalytic domain of glycoside hydrolase (GH) family 5 and a carbohydrate-binding module family 3 (CBM_3). Chromatography using HiTrap Q and CHT-II resulted in the isolation of two truncated forms corresponding to 50 (Cel5L-p50) and 35 kDa (Cel5L-p35, CBM_3-deleted form). Both enzymes were optimally active at pH 4.5 and $55^{\circ}C$, but had different half-lives of 4.0 and 22.8 min, respectively, at $70^{\circ}C$. The relative activities of Cel5L-p50 and Cel5L-p35 for barley ${\beta}$-glucan were 377.0 and 246.7%, respectively, compared to those for carboxymethyl-cellulose. The affinity and hydrolysis rate of pNPC by Cel5L-p35 were 1.7 and 3.3 times higher, respectively, than those by Cel5L-p50. Additions of each to a commercial enzyme set increased saccharification of pretreated rice straw powder by 17.5 and 21.0%, respectively. These results suggest CBM_3 is significantly contributing to thermostability, and to affinity and substrate specificity for small substrates, and that these two enzymes could be used as additives to enhance enzymatic saccharification.

• Parasites, Hosts and Diseases
• /
• v.53 no.1
• /
• pp.65-75
• /
• 2015

Clonorchis sinensis habitating in the bile duct of mammals causes clonorchiasis endemic in East Asian countries. Parkin is a RING-between-RING protein and has E3-ubiquitin ligase activity catalyzing ubiquitination and degradation of substrate proteins. A cDNA clone of C. sinensis was predicted to encode a polypeptide homologous to parkin (CsParkin) including 5 domains (Ubl, RING0, RING1, IBR, and RING2). The cysteine and histidine residues binding to $Zn^{2+}$ were all conserved and participated in formation of tertiary structural RINGs. Conserved residues were also an E2-binding site in RING1 domain and a catalytic cysteine residue in the RING2 domain. Native CsParkin was determined to have an estimated molecular weight of 45.7 kDa from C. sinensis adults by immunoblotting. CsParkin revealed E3-ubiquitin ligase activity and higher expression in metacercariae than in adults. CsParkin was localized in the locomotive and male reproductive organs of C. sinensis adults, and extensively in metacercariae. Parkin has been found to participate in regulating mitochondrial function and energy metabolism in mammalian cells. From these results, it is suggested that CsParkin play roles in energy metabolism of the locomotive organs, and possibly in protein metabolism of the reproductive organs of C. sinensis.

• Journal of Microbiology and Biotechnology
• /
• v.33 no.4
• /
• pp.485-492
• /
• 2023

Methylorubrum extorquens, a facultative methylotroph, assimilates C₁ compounds and accumulates poly-β-hydroxylbutyrate (PHB) as carbon and energy sources. The ethylmalonyl pathway is central to the carbon metabolism of M. extorquens, and is linked with a serine cycle and a PHB biosynthesis pathway. Understanding the ethylmalonyl pathway is vital in utilizing methylotrophs to produce value-added chemicals. In this study, we determined the crystal structure of the mesaconyl-CoA hydratase from M. extorquens (MeMeaC) that catalyzes the reversible conversion of mesaconyl-CoA to β-methylmalyl-CoA. The crystal structure of MeMeaC revealed that the enzyme belongs to the MaoC-like dehydratase domain superfamily and functions as a trimer. In our current MeMeaC structure, malic acid occupied the substrate binding site, which reveals how MeMeaC recognizes the β-methylmalyl-moiety of its substrate. The active site of the enzyme was further speculated by comparing its structure with those of other MaoC-like hydratases.

• BMB Reports
• /
• v.47 no.10
• /
• pp.593-598
• /
• 2014

RNA polymerase II carboxyl-terminal domain (RNAPII CTD) phosphatases are responsible for the dephosphorylation of the C-terminal domain of the small subunit of RNAPII in eukaryotes. Recently, we demonstrated the identification of several interacting partners with human small CTD phosphatase1 (hSCP1) and the substrate specificity to delineate an appearance of the dephosphorylation catalyzed by SCP1. In this study, using the established cells for inducibly expressing hSCP1 proteins, we monitored the modification of ${\beta}$-O-linked N-acetylglucosamine (O-GlcNAc). O-GlcNAcylation is one of the most common post-translational modifications (PTMs). To gain insight into the PTM of hSCP1, we used the Western blot, immunoprecipitation, succinylayed wheat germ agglutinin-precipitation, liquid chromatography-mass spectrometry analyses, and site-directed mutagenesis and identified the $Ser^{41}$ residue of hSCP1 as the O-GlcNAc modification site. These results suggest that hSCP1 may be an O-GlcNAcylated protein in vivo, and its N-terminus may function a possible role in the PTM, providing a scaffold for binding the protein(s).

• Proceedings of the Korea Crystallographic Association Conference
• /
• 2002.11a
• /
• pp.24-24
• /
• 2002

HtrA (high temperature requirement A), a periplasmic heat shock protein, is known to have molecular chaperone function at low temperatures and proteolytic activity at elevated temperatures. To investigate the mechanism of functional switch to pretense, we have determined the crystal structure of the N-terminal protease domain (PD) of HtrA from Thermotoga maritima. HtrA PD shares the same fold with chymotrypsin-like serine professes. However, crystal structure suggests that HtrA PD is not an active pretense at current state since its active site is not formed properly and blocked by an additional helical lid. On the surface of the lid, HtrA PD has hydrophobic patches that could be potential substrate binding sites for molecular chaperone activity. Present structure suggests that the activation of the proteolytic function of HtrA PD at elevated temperatures might occur by the conformational change.

• Journal of Microbiology and Biotechnology
• /
• v.24 no.10
• /
• pp.1413-1420
• /
• 2014

Phytate is an antinutritional factor that impacts the bioavailability of essential minerals such as $Ca^{2+}$, $Mg^{2+}$, $Mn^{2+}$, $Zn^{2+}$, and $Fe^{2+}$ by forming insoluble mineral-phytate salts. These insoluble mineral-phytate salts are hydrolyzed rarely by monogastric animals, because they lack the hydrolyzing phytases and thus excrete the majority of them. The ${\beta}$-propeller phytases (BPPs) hydrolyze these insoluble mineral-phytate salts efficiently. In this study, we cloned a novel BPP gene from a marine Pseudomonas sp. This Pseudomonas BPP gene (PsBPP) had low sequence identity with other known phytases and contained an extra internal repeat domain (residues 24-279) and a typical BPP domain (residues 280-634) at the C-terminus. Structure-based sequence alignment suggested that the N-terminal repeat domain did not possess the active-site residues, whereas the C-terminal BPP domain contained multiple calcium-binding sites, which provide a favorable electrostatic environment for substrate binding and catalytic activity. Thus, we overexpressed the BPP domain from Pseudomonas sp. to potentially hydrolyze insoluble mineral-phytate salts. Purified recombinant PsBPP required $Ca^{2+}$ or $Fe^{2+}$ for phytase activity, indicating that PsBPP hydrolyzes insoluble $Fe^{2+}$-phytate or $Ca^{2+}$-phytate salts. The optimal temperature and pH for the hydrolysis of $Ca^{2+}$-phytate by PsBPP were $50^{\circ}C$ and 6.0, respectively. Biochemical and kinetic studies clearly showed that PsBPP efficiently hydrolyzed $Ca^{2+}$-phytate salts and yielded myo-inositol 2,4,6-trisphosphate and three phosphate groups as final products. Finally, we showed that PsBPP was highly effective for hydrolyzing rice bran with high phytate content. Taken together, our results suggest that PsBPP has great potential in the animal feed industry for reducing phytates.

• 한국생물공학회:학술대회논문집
• /
• 2003.10a
• /
• pp.207-207
• /
• 2003

• Proceedings of the Korean Society of Toxicology Conference
• /
• 2001.10a
• /
• pp.9-9
• /
• 2001

Several micronutrients (vitamins and minerals) are required as co-factors in DNA synthesis, DNA repair, DNA methylation and apoptosis. Some notable examples include (a) folic acid and vitamin B12 required for maintenance methylation of DNA and the synthesis of dTTP from dUTP, thus prevent the misincorporation of uracil into DNA, a highly mutagenic and chromosome-breaking event, (b) niacin, is essential in the form of the coenzymes NAD and NADP which act as a substrate for polyADPribose polymerase (PARP), an enzyme thought to facilitate efficient DNA repair and telomere length regulation and (c) zinc, apart from its antioxidant role as a co-factor in Cu/Zn SOD, it is required in its stabilizing role of the DNA-binding domain of p53 (residues 102-292) and thus is essential for apoptotic response to DNA damage. (omitted)