Aeromonas hydrophila cytosolic 5’-methylthioadenosine/S-adenosylhomocysteine nucleosidase MtaN-2

Jinli Chen,Fei Shang,Lulu Wang,Wei Liu,Yuanyuan Chen,Jing Lan,Liming Jin,Nam-Chul Ha,Chunshan Quan,Yongbin Xu 한국구조생물학회 2018 Biodesign Vol.6 No.3

5’-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) plays a critical role in diverse pathways in bacterial cells such as biological methylation, polyamine biosynthesis, methionine recycling, and bacterial quorum sensing. It has been known that MtaN catalyzes the hydrolysis of N-ribosidic bond of adenosine-based substrates such as S-adenosyl-L-homocysteine (SAH), S-methyl-5’-thioadenosine (MTA) and 5’-deoxyadenosine (5’-DOA). In Aeromonas hydrophila, there are two MtnN subfamily proteins: MtaN-1, a periplasmic protein with an N-terminal signal peptide; and MtaN-2, a cytosolic protein. In this study, MtaN-2 from A. hydrophila was successfully expressed and purified using Ni-NTA affinity, Q anion-exchange, and gel-filtration chromatography. We first crystallized apo MtaN-2 but it diffracted to a low resolution of 5.1 Å. New crystals suitable for diffraction were obtained by adding 2 mM adenosine, a substrate analog of MtaN-2 during purification process and the crystals diffracted to the resolution of 2.0 Å. The crystals belong to the trigonal space group P31 or P32, with unit-cell parameters of a = b = 74.94 Å and c = 185.21 Å. The asymmetric unit contains four complexes of MtaN-2 with hydrolysis products of adenosine.

Crystal structure of <i>E. coli</i> ZinT with one zinc-binding mode and complexed with citrate

Chen, Jinli,Wang, Lulu,Shang, Fei,Dong, Yuesheng,Ha, Nam-Chul,Nam, Ki Hyun,Quan, Chunshan,Xu, Yongbin Elsevier 2018 Biochemical and biophysical research communication Vol.500 No.2

<P><B>Abstract</B></P> <P>The ZnuABC ATP-binding cassette transporter found in gram-negative bacteria has been implicated in ensuring adequate zinc import into Zn(II)-poor environments. ZinT is an essential component of ZnuABC and contributes to metal transport by transferring metals to ZnuA, which delivers them to ZnuB in periplasmic zinc recruitment. Although several structures of <I>E. coli</I> ZinT have been reported, its zinc-binding sites and oligomeric state have not been clearly identified. Here, we report the crystal structure of <I>E. coli</I> ZinT at 1.76 Å resolution. This structure contains one zinc ion in its calycin-like domain, and this ion is coordinated by three highly conserved histidine residues (His167, His176 and His178). Moreover, three oxygen atoms (O<SUB>1</SUB>, O<SUB>6</SUB> and O<SUB>7</SUB>) from the citrate molecule interact with zinc, giving the zinc ion stable octahedral coordination. Our EcZinT structure shows the fewest zinc ions bound of all reported EcZinT structures. Crystallographic packing and size exclusion chromatography suggest that EcZinT prefers to form monomers in solution. Our results provide insights into the molecular function of ZinT.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Crystal structure of <I>E. coli</I> ZinT complexed with citrate in one zinc-binding mode. </LI> <LI> The bound zinc shows octahedral coordination by histidine residues and citrate. </LI> <LI> EcZinT exists as a monomer in solution in the absence and presence of zinc ions. </LI> </UL> </P>

Bacillus amyloliquefaciens NAD+-dependent protein deacetylase: purification, crystallization and X-ray crystallographic analysis

Fei Shang,Jinli Chen,Lulu Wang,Yuanyuan Chen,Jing Lan,Wei Liu,Liming Jin,하남철,Chunshan Quan,Yongbin Xu 한국구조생물학회 2019 Biodesign Vol.7 No.1

Sirtuins are NAD+-dependent deacetylase that are broadly conserved throughout bacteria, archaea, and eukaryotes. Themembers of sirtuins are important in regulating diverse biological pathways, including gene silencing, DNA repair, genomestability, longevity, metabolism, and cell physiology. Sirtuin from Bacillus amyloliquefaciens (BaSrtN) is a particularlyinteresting bacterial Sir2 homologue. In this study, to further understand the function and mechanisms of this protein,BaSrtN was successfully expressed and purified using Ni-NTA affinity, Q anion-exchange, and gel-filtration chromatography. Purified BaSrtN was crystallized and diffracted to the resolution of 1.45 Å. The preliminary crystallographic analysissuggested that BaSrtN crystal belongs to the trigonal space group P31 or P32, with unit-cell parameters of a = b = 90.115and c = 86.306 Å. Size-exclusion chromatography suggested that BaSrtN prefer to exit as monomers in solution.

One-Pot Synthesis of Nanodendritic PtIr Alloy with High Electrochemical Activity for Ethylene Glycol Oxidation

Xuedong Gao,Lulu Liu,Qiyu Wang,Kun Qi,Zhao Jin,WEITAO ZHENG,XIAOQIANG CUI 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2017 NANO Vol.12 No.2

Nanodendritic Pt-based bimetallic alloys are one promising catalyst with three-dimensional (3D) networks structure composed of integrating branches for electrochemical catalytic reaction. We successfully synthesized dendrites Pt6Ir4 alloy with small size of 20 nm in oleylamine. The dendritic Pt6Ir4 alloy are characterized by high-resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). The electrochemical tests suggest that the as-prepared dendritic Pt6Ir4 alloy exhibits greatly enhanced ethylene glycol oxidation reaction (EGOR) activity than commercial Pt/C with high EGOR mass activity, anti-poisoning and stability.

Electrochemical property of graphene oxide/polyaniline composite prepared by in situ interfacial polymerization

Nguyen, Van Hoa,Tang, Lulu,Shim, Jae-Jin Springer-Verlag 2013 Colloid and polymer science Vol.291 No.9

Data Recovery Method for Seafood Quality Safety System Based on Rough Set Theory

Xu E,Shuang Lin,Lulu Jin 보안공학연구지원센터 2014 International Journal of Security and Its Applicat Vol.8 No.5

Crystal structure of the nicotinamidase/pyrazinamidase PncA from <i>Bacillus subtilis</i>

Shang, Fei,Chen, Jinli,Wang, Lulu,Jin, Liming,Zou, Linhai,Bu, Tingting,Dong, Yuesheng,Ha, Nam-Chul,Nam, Ki Hyun,Quan, Chunshan,Xu, Yongbin Elsevier 2018 Biochemical and biophysical research communication Vol.503 No.4

<P><B>Abstract</B></P> <P>The nicotinamidase/pyrazinamidase PncA is a member of a large family of hydrolase enzymes that catalyze the deamination of nicotinamide to nicotinic acid. PncA also functions as a pyrazinamidase in a wide variety of eubacteria and is an essential coenzyme in many cellular redox reactions in living systems. We report the crystal structure of substrate-free PncA from <I>Bacillus subtilis</I> (BsPncA) at 2.0 Å resolution to improve our understanding of the PncA family. The structure of BsPncA consists of an α/β domain and a subdomain. The subdomain of BsPncA has a different conformation than that of PncA enzymes from other organisms. The B-factor analysis revealed a rigid structure of the α/β domain, while the subdomain is highly flexible. Both dimers and tetramers were observed in BsPncA protein crystals, but only dimers were observed in solution. Our results provide useful information that will further enhance our understanding of the molecular functions of PncA family members.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Crystal structure of <I>B. Subtilis</I> PncA consists of an α/β domain and a subdomain. </LI> <LI> The metal-binding site of BsPncA is located at the bottom of a large cavity between the core and the subdomain. </LI> <LI> Zinc ion is pentahedrally coordinated within several highly conserved amino acid residues and one water molecule. </LI> <LI> Both dimers and tetramers were observed in BsPncA protein crystals, but only dimers were observed in solution. </LI> </UL> </P>

Structural and Functional Analyses of Periplasmic 5′-Methylthioadenosine/<i>S</i>-Adenosylhomocysteine Nucleosidase from <i>Aeromonas hydrophila</i>

Xu, Yongbin,Wang, Lulu,Chen, Jinli,Zhao, Jing,Fan, Shengdi,Dong, Yuesheng,Ha, Nam-Chul,Quan, Chunshan American Chemical Society 2017 Biochemistry Vol.56 No.40

<P>The Gram-negative, rod-shaped bacterium Aeromonas hydrophila has two multifunctional 5/-methylthioadenosine/S-adenosylhomocysteine nucleosidase (MTAN) enzymes, MtaN-1 and MtaN-2, that differ from those in other bacteria. These proteins are essential for several metabolic pathways, including biological methylation, polyamine biosynthesis, methionine recycling, and bacterial quorum sensing. To gain insight into how these two proteins function, we determined four high-resolution crystal structures of MtaN-1 in its apo form and in complex with the substrates S-adenosyl-L-homocysteine, S'-methylthioadenosine, and 5'-deoxyadenosine. We found that the domain structures were generally similar, although slight differences were evident. The crystal structure demonstrates that AhMtaN-1 has an extension of the binding pocket and revealed that a tryptophan in the active site (Trp199) may playa major role in substrate binding, unlike in other MTAN proteins. Mutation of the Trp199 residue completely abolished the enzyme activity. Trp199 was identified as an active site residue that is essential for catalysis. Furthermore, biochemical characterization of AhMtaN-1 and AhMtaN-2 demonstrated that AhMtaN-1 exhibits inherent trypsin resistance that is higher than that of AhMtaN-2. Additionally, the thermally unfolded AhMtaN-2 protein is capable of refolding into active forms, whereas the thermally unfolded AhMtaN-1 protein does not have this ability. Examining the different biochemical characteristics related to the functional roles of AhMtaN-1 and AhMtaN-2 would be interesting. Indeed, the biochemical characterization of these structural features would provide a structural basis for the design of new antibiotics against A. hydrophila.</P>

Schisandrin A ameliorates MPTP‑induced Parkinson’s disease in a mouse model via regulation of brain autophagy

Yinghao Zhi,Yongxi Jin,Lulu Pan,Aiguo Zhang 대한약학회 2019 Archives of Pharmacal Research Vol.42 No.11

Schisandrin A (Sch A) is one of the principalbioactive lignans isolated from Fructus schisandrae. In thisstudy, we demonstrated its protective effect and biochemicalmechanism of action in a 1-methyl-4-phenyl-1, 2, 3,6-tetrahydropyridine-induced mouse model of Parkinson’sdisease. Sch A significantly ameliorated behavioural abnormalitiesand increased the number of nigral dopaminergicneurons detected by tyrosine hydroxylase immunohistochemistry. Pre-treatment with Sch A significantly decreasedthe levels of the inflammatory mediators IL-6, IL-1β, andTNF-α and markedly improved antioxidant defences byinhibiting the activity of MDA and increasing that of SOD. Furthermore, Sch A activated expression of the autophagyrelatedproteins LC3-II, beclin1, parkin, and PINK1 andincreased mTOR expression. Taken together, these findingsindicate that Sch A has neuroprotective effects against thedevelopment of Parkinson’s disease via regulation of brainautophagy.

Omp16, a conserved peptidoglycan-associated lipoprotein, is involved in Brucella virulence in vitro

Feijie Zhi,Dong Zhou,Junmei Li,Lulu Tian,Guangdong Zhang,Yaping Jin,Aihua Wang 한국미생물학회 2020 The journal of microbiology Vol.58 No.9

Brucella, the bacterial agent of common zoonotic brucellosis, primarily infects specific animal species. The Brucella outer membrane proteins (Omps) are particularly attractive for developing vaccine and improving diagnostic tests and are associated with the virulence of smooth Brucella strains. Omp16 is a homologue to peptidoglycan-associated lipoproteins (Pals), and an omp16 mutant has not been generated in any Brucella strain until now. Very little is known about the functions and pathogenic mechanisms of Omp16 in Brucella. Here, we confirmed that Omp16 has a conserved Pal domain and is highly conserved in Brucella. We attempted to delete omp16 in Brucella suis vaccine strain 2 (B. suis S2) without success, which shows that Omp16 is vital for Brucella survival. We acquired a B. suis S2 Omp16 mutant via conditional complementation. Omp16 deficiency impaired Brucella outer membrane integrity and activity in vitro. Moreover, inactivation of Omp16 decreased bacterial intracellular survival in macrophage RAW 264.7 cells. B. suis S2 and its derivatives induced marked expression of IL-1β, IL-6, and TNF-α mRNA in Raw 264.7 cells. Whereas inactivation of Omp16 in Brucella enhanced IL-1β and IL-6 expression in Raw 264.7 cells. Altogether, these findings show that the Brucella Omp16 mutant was obtained via conditional complementation and confirmed that Omp16 can maintain outer membrane integrity and be involved in bacterial virulence in Brucella in vitro and in vivo. These results will be important in uncovering the pathogenic mechanisms of Brucella.