Structural insight into the carboxylesterase BioH from <i>Klebsiella pneumoniae</i>

Wang, Lulu,Chen, Yuanyuan,Shang, Fei,Liu, Wei,Lan, Jing,Gao, Peng,Ha, Nam-Chul,Nam, Ki Hyun,Dong, Yuesheng,Quan, Chunshan,Xu, Yongbin Elsevier 2019 Biochemical and biophysical research communication Vol.520 No.3

<P><B>Abstract</B></P> <P>The BioH carboxylesterase which is a typical α/β-hydrolase enzyme involved in biotin synthetic pathway in most bacteria. BioH acts as a gatekeeper and blocks the further elongation of its substrate. In the pathogen <I>Klebsiella pneumoniae</I>, BioH plays a critical role in the biosynthesis of biotin. To better understand the molecular function of BioH, we determined the crystal structure of BioH from <I>K. pneumoniae</I> at 2.26 Å resolution using X-ray crystallography. The structure of KpBioH consists of an α-β-α sandwich domain and a cap domain. B-factor analysis revealed that the α-β-α sandwich domain is a rigid structure, while the loops in the cap domain shows the structural flexibility. The active site of KpBioH contains the catalytic triad (Ser82-Asp207-His235) on the interface of the α-β-α sandwich domain, which is surrounded by the cap domain. Size exclusion chromatography shows that KpBioH prefers the monomeric state in solution, whereas two-fold symmetric dimeric formation of KpBioH was observed in the asymmetric unit, the conserved Cys31-based disulfide bonds can maintain the irreversible dimeric formation of KpBioH. Our study provides important structural insight for understanding the molecular mechanisms of KpBioH and its homologous proteins.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Crystal structure of <I>K. pneumoniae</I>BioH consists of an α-β-αsandwish domain and acapsubdomain. </LI> <LI> The active site of KpBioH contains the catalytic triad (Ser82-Asp207-His235). </LI> <LI> The Arg138, Arg142, Arg155, and Arg159 of KpBioH may play an important role in the binding of the substrates like ACP. </LI> <LI> The Cys31-based disulfide bonds can maintain the irreversible dimeric formation of KpBioH. </LI> </UL> </P>

Cytosolic 5′-Methylthioadenosine/ S-Adenosylhomocysteine Nucleosidase MtaN from Mycobacterium. smegmatis: purification, crystallization and X-ray crystallographic analysis

Lulu Wang,Yuanyuan Chen,Wei Liu,Jing Lan,Fei Shang,Nam-Chul Ha,Yuesheng Dong,Chunshan Quan,Yongbin Xu 한국구조생물학회 2019 Biodesign Vol.7 No.3

Mycobacterium tuberculosis is a dangerous pathogen, and it can cause the most deadly disease tuberculosis (TB). Nonpathogenic Mycobacterium smegmatis is an important model for studying the M. tuberculosis. M. smegmatis 5’-Methylthioadenosine/S-adenosyl-L-homocysteine nucleosidases (MtaNs) catalyze the hydrolysis of adenine from 5’-methylthioadenosine (MTA), MtaNs cleave the glycosidic bond of MTA or S-adenosylhomocysteine (SAH) irreversibly. In this study, MtaN from M. smegmatis (MsMtaN) was successfully expressed and purified using Ni-NTA affinity, Q anionexchange and gel-filtration chromatography. The protein crystal was obtained and diffracted to a resolution of 2.0 Å. The crystal belonged to the orthorhombic space group P1211, with unit-cell parameters of a =57.6, b = 172.6, and c = 183.3 Å. The Matthews coefficient and solvent content were estimated to be 2.32 Å3 Da-1 and 47%, respectively, assuming that the asymmetric unit contained only one recombinant protein molecule. Size-exclusion chromatography suggested that MsMtaN prefer to exist as tetramer in solution.

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>

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>

Hexameric assembly of membrane fusion protein YknX of the sporulation delaying efflux pump from <i>Bacillus amyloliquefaciens</i>

Xu, Yongbin,Jo, Inseong,Wang, Lulu,Chen, Jinli,Fan, Shengdi,Dong, Yuesheng,Quan, Chunshan,Ha, Nam-Chul Elsevier 2017 Biochemical and biophysical research communication Vol.493 No.1

<P><B>Abstract</B></P> <P>Membrane fusion proteins (MFPs) play an essential role in the action of the drug efflux pumps and protein secretion systems in bacteria. The sporulation delaying protein (SDP) efflux pump YknWXYZ has been identified in diverse <I>Bacillus</I> species. The MFP YknX requires the ATP-binding cassette (ABC) transporter YknYZ and the Yip1 family protein YknW to form a functional complex. To date, the crystal structure, molecular function and mechanism of action of YknX remain unknown. In this study, to characterize the structural and biochemical roles of YknX in the functional assembly of YknWXYZ from <I>B. amyloliquefaciens</I>, we successfully obtained crystals of the YknX protein that diffracted X-rays to a resolution of 4.4 Å. We calculated an experimentally phased map using single-wavelength anomalous diffraction (SAD), revealing that YknX forms a hexameric assembly similar to that of MacA from Gram-negative bacteria. The hexameric assembly of YknX exhibited a funnel-like structure with a central channel and a conical mouth. Functional studies <I>in vitro</I> suggest that YknX can bind directly to peptidoglycan. Our study provides an improved understanding of the assembly of the YknWXYZ efflux pump and the role of YknX in the complex.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The functional and structural properties of the YknX from <I>B. amyloliquefaciens.</I> </LI> <LI> The three-dimensional structure of MFP YknX and it has a strong affinity toward peptidoglycan. </LI> <LI> The YknX may forms a hexameric assembly in the crystal packing. </LI> <LI> The YknX displayed a similar upside-down, funnel-shaped orientation as <I>Aa</I> MacA. </LI> </UL> </P>

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>

Effects of Different Atmosphere on Electrochemical Performance of Hard Carbon Electrode in Sodium Ion Battery

Ziqiang Xu,Jinchen Chen,Mengqiang Wu,Cheng Chen,Yaochen Song,Yuesheng Wang 대한금속·재료학회 2019 ELECTRONIC MATERIALS LETTERS Vol.15 No.4

Hard carbon is deemed to be a most promising anode materials for sodium—ion batteries (SIBs), while, the issues of lowcapacity and low initial coulombic efficiency still exist limiting the development of SIBs. Although high temperature carbonizationof biomass materials under nitrogen or argon atmosphere is a common method for preparation of hard carbon,there are few reports about the effects of different protective atmospheres on propriety of hard carbon. In this article, hornet’snest (HN) is used to prepare hard carbon under nitrogen and argon. At a suitable carbonization temperature (1200 °C and1400 °C), the hard carbon under argon possesses lower specific surface area (25–50 cm−3 g−1), but higher initial coulombefficiency (4–6%) and higher capacity retention (3–6%). Thus, it is inferred that high—performance hard carbon can beobtained under argon atmosphere. Our research about the effect of sintering atmosphere on material properties is expectedto provide a reference for the synthetization of hard carbon by high temperature carbonization.

Amorphous iron phosphate: potential host for various charge carrier ions

Mathew, Vinod,Kim, Sungjin,Kang, Jungwon,Gim, Jihyeon,Song, Jinju,Baboo, Joseph Paul,Park, Wangeun,Ahn, Docheon,Han, Junhee,Gu, Lin,Wang, Yuesheng,Hu, Yong-Sheng,Sun, Yang-Kook,Kim, Jaekook Springer Science and Business Media LLC 2014 NPG Asia Materials Vol.6 No.-