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Mammalian cyclic GMP-AMP synthase (cGAS) and its homologue dinucleotide cyclase in Vibrio cholerae (VcDncV) produce cyclic dinucleotides (CDNs) that participate in the defense against viral infection. Recently, scores of new cGAS/DncV-like nucleotidyltransferases (CD-NTases) were discovered, which produce various CDNs and cyclic trinucleotides (CTNs) as second messengers. Here, we present the crystal structures of EcCdnD, a CD-NTase from Enterobacter cloacae that produces cyclic AMP-AMP-GMP, in its apo-form and in complex with ATP, ADP and AMPcPP, an ATP analogue. Despite the similar overall architecture, the protein shows significant structural variations from other CD-NTases. Adjacent to the donor substrate, another nucleotide is bound to the acceptor binding site by a non-productive mode. Isothermal titration calorimetry results also suggest the presence of two ATP binding sites. GTP alone does not bind to EcCdnD, which however binds to pppApG, a possible intermediate. The enzyme is active on ATP or a mixture of ATP and GTP, and the best metal cofactor is Mg2+. The conserved residues Asp69 and Asp71 are essential for catalysis, as indicated by the loss of activity in the mutants. Based on structural analysis and comparison with VcDncV and RNA polymerase, a tentative catalytic pathway for the CTN-producing EcCdnD is proposed.
Tzu-Ping Ko; Yu-Chuan Wang; Chia-Ling Tsai; Chia-Shin Yang; Mei-Hui Hou; Yeh Chen. Crystal structure and functional implication of a bacterial cyclic AMP–AMP–GMP synthetase. Nucleic Acids Research 2021, 49, 4725 -4737.
AMA StyleTzu-Ping Ko, Yu-Chuan Wang, Chia-Ling Tsai, Chia-Shin Yang, Mei-Hui Hou, Yeh Chen. Crystal structure and functional implication of a bacterial cyclic AMP–AMP–GMP synthetase. Nucleic Acids Research. 2021; 49 (8):4725-4737.
Chicago/Turabian StyleTzu-Ping Ko; Yu-Chuan Wang; Chia-Ling Tsai; Chia-Shin Yang; Mei-Hui Hou; Yeh Chen. 2021. "Crystal structure and functional implication of a bacterial cyclic AMP–AMP–GMP synthetase." Nucleic Acids Research 49, no. 8: 4725-4737.
Bacterial wall teichoic acids (WTAs) are synthesized intracellularly and exported by a two-component transporter, TagGH, comprising the transmembrane and ATPase subunits TagG and TagH. Here the dimeric structure of the N-terminal domain of TagH (TagH-N) was solved by single-wavelength anomalous diffraction using a selenomethionine-containing crystal, which shows an ATP-binding cassette (ABC) architecture with RecA-like and helical subdomains. Besides significant structural differences from other ABC transporters, a prominent patch of positively charged surface is seen in the center of the TagH-N dimer, suggesting a potential binding site for the glycerol phosphate chain of WTA. The ATPase activity of TagH-N was inhibited by clodronate, a bisphosphonate, in a non-competitive manner, consistent with the proposed WTA-binding site for drug targeting.
Chia-Shin Yang; Wei-Chien Huang; Tzu-Ping Ko; Yu-Chuan Wang; Andrew H.-J. Wang; Yeh Chen. Crystal structure of the N-terminal domain of TagH reveals a potential drug targeting site. Biochemical and Biophysical Research Communications 2020, 536, 1 -6.
AMA StyleChia-Shin Yang, Wei-Chien Huang, Tzu-Ping Ko, Yu-Chuan Wang, Andrew H.-J. Wang, Yeh Chen. Crystal structure of the N-terminal domain of TagH reveals a potential drug targeting site. Biochemical and Biophysical Research Communications. 2020; 536 ():1-6.
Chicago/Turabian StyleChia-Shin Yang; Wei-Chien Huang; Tzu-Ping Ko; Yu-Chuan Wang; Andrew H.-J. Wang; Yeh Chen. 2020. "Crystal structure of the N-terminal domain of TagH reveals a potential drug targeting site." Biochemical and Biophysical Research Communications 536, no. : 1-6.
During the microbial degradation of borneol, a bicyclic plant monoterpene, it is first converted into camphor by borneol dehydrogenase (BDH) and then enters a known camphor-degradation pathway. Previously, a recombinant Pseudomonas BDH was found in inclusion bodies when expressed in Escherichia coli. After refolding, it was still unstable and was difficult to concentrate. Here, the protein-expression conditions were improved by changing the medium from lysogeny broth to Terrific Broth, yielding a soluble form of the enzyme with higher activity. The protein was crystallized and its 3D structure was determined by X-ray diffraction. Like other known homologues such as quinuclidinone reductase, the protein forms a tetramer with subunits containing Rossmann folds. Structural comparison revealed major differences in the C-terminal helices and the associated loops. It is likely that these regions contain the determinants for substrate recognition.
Aye Aye Khine; Hao-Ping Chen; Kai-Fa Huang; Tzu-Ping Ko. Structural characterization of borneol dehydrogenase from Pseudomonas sp. TCU-HL1. Acta Crystallographica Section F Structural Biology Communications 2020, 76, 309 -313.
AMA StyleAye Aye Khine, Hao-Ping Chen, Kai-Fa Huang, Tzu-Ping Ko. Structural characterization of borneol dehydrogenase from Pseudomonas sp. TCU-HL1. Acta Crystallographica Section F Structural Biology Communications. 2020; 76 (7):309-313.
Chicago/Turabian StyleAye Aye Khine; Hao-Ping Chen; Kai-Fa Huang; Tzu-Ping Ko. 2020. "Structural characterization of borneol dehydrogenase from Pseudomonas sp. TCU-HL1." Acta Crystallographica Section F Structural Biology Communications 76, no. 7: 309-313.
Thebaine synthase 2 (THS2) that can transform (7S)-salutaridinol 7-O-acetate to thebaine catalyzes the final step of thebaine biosynthesis in Papaver somniferum. Here, the crystal structures of THS2 and its complex with thebaine are reported, revealing the interaction network in the substrate-binding pocket. Subsequent docking and QM/MM studies was performed to further explore the catalytic mechanism of THS2. Our results suggest that T105 may abstract the proton of C4–OH from the substrate under the assistance of H89. The resulting C4–O- phenolate anion then attacks the nearby C5, and triggers intramolecular SN2′ syn displacement with the elimination of O-acetyl group. Moreover, the latter SN2′ reaction is the rate-determining step of the whole enzymatic reaction with an overall energy barrier of 18.8 kcal/mol. These findings are of pivotal importance to understand the mechanism of action of thebaine biosynthesis, and would guide enzyme engineering to enhance the production of opiate alkaloids via metabolic engineering.
Chun-Chi Chen; Jing Xue; Wei Peng; Binju Wang; Lilan Zhang; Weidong Liu; Tzu-Ping Ko; Jian-Wen Huang; Shuyu Zhou; Jian Min; Lixin Ma; Longhai Dai; Rey-Ting Guo; Xuejing Yu. Structural insights into thebaine synthase 2 catalysis. Biochemical and Biophysical Research Communications 2020, 529, 156 -161.
AMA StyleChun-Chi Chen, Jing Xue, Wei Peng, Binju Wang, Lilan Zhang, Weidong Liu, Tzu-Ping Ko, Jian-Wen Huang, Shuyu Zhou, Jian Min, Lixin Ma, Longhai Dai, Rey-Ting Guo, Xuejing Yu. Structural insights into thebaine synthase 2 catalysis. Biochemical and Biophysical Research Communications. 2020; 529 (2):156-161.
Chicago/Turabian StyleChun-Chi Chen; Jing Xue; Wei Peng; Binju Wang; Lilan Zhang; Weidong Liu; Tzu-Ping Ko; Jian-Wen Huang; Shuyu Zhou; Jian Min; Lixin Ma; Longhai Dai; Rey-Ting Guo; Xuejing Yu. 2020. "Structural insights into thebaine synthase 2 catalysis." Biochemical and Biophysical Research Communications 529, no. 2: 156-161.
Uracil-DNA glycosylases (UDGs) are conserved DNA-repair enzymes that can be found in many species, including herpesviruses. Since they play crucial roles for efficient viral DNA replication in herpesviruses, they have been considered as potential antiviral targets. In our previous work, Staphylococcus aureus SAUGI was identified as a DNA mimic protein that targets UDGs from S. aureus, human, Herpes simplex virus (HSV) and Epstein-Barr virus (EBV). Interestingly, SAUGI has the strongest inhibitory effects with EBVUDG. Here, we determined complex structures of SAUGI with EBVUDG and another γ-herpesvirus UDG from Kaposi's sarcoma-associated herpesvirus (KSHVUDG), which SAUGI fails to effectively inhibit. Structural analysis of the SAUGI/EBVUDG complex suggests that the additional interaction between SAUGI and the leucine loop may explain why SAUGI shows the highest binding capacity with EBVUDG. In contrast, SAUGI appears to make only partial contacts with the key components responsible for the compression and stabilization of the DNA backbone in the leucine loop extension of KSHVUDG. The findings in this study provide a molecular explanation for the differential inhibitory effects and binding strengths that SAUGI has on these two UDGs, and the structural basis of the differences should be helpful in developing inhibitors that would interfere with viral DNA replication.
Yi-Ting Liao; Shin-Jen Lin; Tzu-Ping Ko; Chang-Yi Liu; Kai-Cheng Hsu; Hao-Ching Wang. Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases. International Journal of Biological Macromolecules 2020, 160, 903 -914.
AMA StyleYi-Ting Liao, Shin-Jen Lin, Tzu-Ping Ko, Chang-Yi Liu, Kai-Cheng Hsu, Hao-Ching Wang. Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases. International Journal of Biological Macromolecules. 2020; 160 ():903-914.
Chicago/Turabian StyleYi-Ting Liao; Shin-Jen Lin; Tzu-Ping Ko; Chang-Yi Liu; Kai-Cheng Hsu; Hao-Ching Wang. 2020. "Structural insight into the differential interactions between the DNA mimic protein SAUGI and two gamma herpesvirus uracil-DNA glycosylases." International Journal of Biological Macromolecules 160, no. : 903-914.
Cytochrome P450 monooxygenases are versatile heme-thiolate enzymes that catalyze a wide range of reactions. Self-sufficient cytochrome P450 enzymes contain the redox partners in a single polypeptide chain. Here, we present the crystal structure of full-length CYP116B46, a self-sufficient P450. The continuous polypeptide chain comprises three functional domains, which align well with the direction of electrons traveling from FMN to the heme through the [2Fe-2S] cluster. FMN and the [2Fe-2S] cluster are positioned closely, which facilitates efficient electron shuttling. The edge-to-edge straight-line distance between the [2Fe-2S] cluster and heme is approx. 25.3 Å. The role of several residues located between the [2Fe-2S] cluster and heme in the catalytic reaction is probed in mutagenesis experiments. These findings not only provide insights into the intramolecular electron transfer of self-sufficient P450s, but are also of interest for biotechnological applications of self-sufficient P450s.
Lilan Zhang; Zhenzhen Xie; Ziwei Liu; Shuyu Zhou; Lixin Ma; Weidong Liu; Jian-Wen Huang; Tzu-Ping Ko; Xiuqin Li; Yuechan Hu; Jian Min; Xuejing Yu; Rey-Ting Guo; Chun-Chi Chen. Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase. Nature Communications 2020, 11, 1 .
AMA StyleLilan Zhang, Zhenzhen Xie, Ziwei Liu, Shuyu Zhou, Lixin Ma, Weidong Liu, Jian-Wen Huang, Tzu-Ping Ko, Xiuqin Li, Yuechan Hu, Jian Min, Xuejing Yu, Rey-Ting Guo, Chun-Chi Chen. Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase. Nature Communications. 2020; 11 (1):1.
Chicago/Turabian StyleLilan Zhang; Zhenzhen Xie; Ziwei Liu; Shuyu Zhou; Lixin Ma; Weidong Liu; Jian-Wen Huang; Tzu-Ping Ko; Xiuqin Li; Yuechan Hu; Jian Min; Xuejing Yu; Rey-Ting Guo; Chun-Chi Chen. 2020. "Structural insight into the electron transfer pathway of a self-sufficient P450 monooxygenase." Nature Communications 11, no. 1: 1.
When administrated orally, the vasodilating drug diltiazem can be metabolized into diacetyl diltiazem in the presence of Bacteroides thetaiotaomicron, a human gut microbe. The removal of acetyl group from the parent drug is carried out by the GDSL/SGNH-family hydrolase BT4096. Here the crystal structure of the enzyme was solved by mercury soaking and single-wavelength anomalous diffraction. The protein folds into two parts. The N-terminal part comprises the catalytic domain which is similar to other GDSL/SGNH hydrolases. The flanking C-terminal part is made up of a β-barrel subdomain and an α-helical subdomain. Structural comparison shows that the catalytic domain is most akin to acetyl-xylooligosaccharide esterase and allows a plausible binding mode of diltiazem to be proposed. The β-barrel subdomain is similar in topology to the immunoglobulin-like domains, including some carbohydrate-binding modules, of various bacterial glycoside hydrolases. Consequently, BT4096 might originally function as an oligosaccharide deacetylase with additional subdomains that could enhance substrate binding, and it acts on diltiazem just by accident.
Shuyu Zhou; Tzu-Ping Ko; Jian-Wen Huang; Weidong Liu; Yingying Zheng; Shan Wu; Qian Wang; Zhenzhen Xie; Ziwei Liu; Chun-Chi Chen; Rey-Ting Guo. Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode. Biochemical and Biophysical Research Communications 2020, 527, 799 -804.
AMA StyleShuyu Zhou, Tzu-Ping Ko, Jian-Wen Huang, Weidong Liu, Yingying Zheng, Shan Wu, Qian Wang, Zhenzhen Xie, Ziwei Liu, Chun-Chi Chen, Rey-Ting Guo. Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode. Biochemical and Biophysical Research Communications. 2020; 527 (3):799-804.
Chicago/Turabian StyleShuyu Zhou; Tzu-Ping Ko; Jian-Wen Huang; Weidong Liu; Yingying Zheng; Shan Wu; Qian Wang; Zhenzhen Xie; Ziwei Liu; Chun-Chi Chen; Rey-Ting Guo. 2020. "Structure of a gut microbial diltiazem-metabolizing enzyme suggests possible substrate binding mode." Biochemical and Biophysical Research Communications 527, no. 3: 799-804.
Isoprenyl diphosphate synthases (IDSs) catalyze condensation reactions of isoprene units to produce isoprenoids or terpenoids, the largest class of natural products on earth. IDSs are divided into trans- and cis-IDS superfamilies depending on the configuration of the resulting carbon-carbon double bonds. Compared to trans-IDSs, cis-IDS family members exhibit more variable active site structure and versatile function. The archetypal cis-IDSs are homodimers and produce linear isoprenoids via head-to-tail condensation. Recently, heterodimeric cis-IDSs containing a non-catalytic subunit that also belongs to the cis-IDS superfamily have been identified. Moreover, several cis-IDS-fold members have been found to produce non-linear isoprenoids via “head-to-middle” condensation. In this review, we summarize the structural features and catalytic mechanism of the versatile cis-IDS superfamily. This information provide important guidance for research regarding biosynthesis of important natural products and medical intermediates, cellular metabolism and disease control.
Chun-Chi Chen; Lilan Zhang; Xuejing Yu; Lixin Ma; Tzu-Ping Ko; Rey-Ting Guo. Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation. ACS Catalysis 2020, 10, 4717 -4725.
AMA StyleChun-Chi Chen, Lilan Zhang, Xuejing Yu, Lixin Ma, Tzu-Ping Ko, Rey-Ting Guo. Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation. ACS Catalysis. 2020; 10 (8):4717-4725.
Chicago/Turabian StyleChun-Chi Chen; Lilan Zhang; Xuejing Yu; Lixin Ma; Tzu-Ping Ko; Rey-Ting Guo. 2020. "Versatile cis-isoprenyl Diphosphate Synthase Superfamily Members in Catalyzing Carbon–Carbon Bond Formation." ACS Catalysis 10, no. 8: 4717-4725.
Feline infectious peritonitis virus (FIPV) is an alphacoronavirus that causes a nearly 100% mortality rate without effective treatment. Here we report a 3.3-Å cryoelectron microscopy (cryo-EM) structure of the serotype I FIPV spike (S) protein, which is responsible for host recognition and viral entry. Mass spectrometry provided site-specific compositions of densely distributed high-mannose and complex-type N-glycans that account for 1/4 of the total molecular mass; most of the N-glycans could be visualized by cryo-EM. Specifically, the N-glycans that wedge between 2 galectin-like domains within the S1 subunit of FIPV S protein result in a unique propeller-like conformation, underscoring the importance of glycosylation in maintaining protein structures. The cleavage site within the S2 subunit responsible for activation also showed distinct structural features and glycosylation. These structural insights provide a blueprint for a better molecular understanding of the pathogenesis of FIP.
Tzu-Jing Yang; Yen-Chen Chang; Tzu-Ping Ko; Piotr Draczkowski; Yu-Chun Chien; Yuan-Chih Chang; Kuen-Phon Wu; Kay-Hooi Khoo; Hui-Wen Chang; Shang-Te Danny Hsu. Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans. Proceedings of the National Academy of Sciences 2020, 117, 1438 -1446.
AMA StyleTzu-Jing Yang, Yen-Chen Chang, Tzu-Ping Ko, Piotr Draczkowski, Yu-Chun Chien, Yuan-Chih Chang, Kuen-Phon Wu, Kay-Hooi Khoo, Hui-Wen Chang, Shang-Te Danny Hsu. Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans. Proceedings of the National Academy of Sciences. 2020; 117 (3):1438-1446.
Chicago/Turabian StyleTzu-Jing Yang; Yen-Chen Chang; Tzu-Ping Ko; Piotr Draczkowski; Yu-Chun Chien; Yuan-Chih Chang; Kuen-Phon Wu; Kay-Hooi Khoo; Hui-Wen Chang; Shang-Te Danny Hsu. 2020. "Cryo-EM analysis of a feline coronavirus spike protein reveals a unique structure and camouflaging glycans." Proceedings of the National Academy of Sciences 117, no. 3: 1438-1446.
Flavonoids are well-known antioxidants and have shown the ability to prevent tumor formation and recurrence. Especially in dietary flavonoids, they have provided convenience and consistence of intake for long-term prevention of tumor formation. Previous reports suggested that S100 calcium-binding protein A7 (S100A7) might activate epithelial–mesenchymal transition (EMT) signaling and promote the metastasis of tumor cells; however, the regulatory signaling was unclear. In this study, we found that S100A7 was highly expressed in cancer cells and could be reduced by luteolin (Lu) and quercetin (Qu) through Src/Stat3 signaling. We found that the protein levels of S100A7, phosphorylated Src (p-Src), and p-Stat3 were increased in A431-III cells. Flavonoids Lu and Qu reduce protein levels of p-Src, p-Stat3 and S100A7 in A431-III cells. Treatment of A431-III cells with Src inhibitor SU6656 and Stat3 inhibitor S3I-201 also reduced the protein levels of S100A7. Transactivation activity of 5′-upstream regions of S100A7 was activated by Stat3 but was reduced by treatment with Lu, Qu, SU6656 and S3I-201. The treatment also reduced the migratory and invasive abilities of A431-III cells. In a further analysis of EMT markers, the protein level of E-cad increased and that of Twist decreased after treatment with the inhibitors and flavonoids. Overexpression of S100A7 decreased the protein level of E-cad and increased the Twist level, whereas knockdown of S100A7 had the opposite effects. Treatment with S3I-201, Lu and Qu, compared to the control, were found to decrease metastasis of tumor cells in zebrafish larvae. These results suggest that Lu and Qu may inhibit Src/Stat3/S100A7 signaling to reduce tumorigenesis of cancer cells.
Jhen-Jia Fan; Wen-Hsien Hsu; Kuen-Haur Lee; Ku-Chung Chen; Cheng-Wei Lin; Yu-Lin A Lee; Tzu-Ping Ko; Lang-Ta Lee; Ming-Ting Lee; Mau-Sun Chang; Chia-Hsiung Cheng. Dietary Flavonoids Luteolin and Quercetin Inhibit Migration and Invasion of Squamous Carcinoma through Reduction of Src/Stat3/S100A7 Signaling. Antioxidants 2019, 8, 557 .
AMA StyleJhen-Jia Fan, Wen-Hsien Hsu, Kuen-Haur Lee, Ku-Chung Chen, Cheng-Wei Lin, Yu-Lin A Lee, Tzu-Ping Ko, Lang-Ta Lee, Ming-Ting Lee, Mau-Sun Chang, Chia-Hsiung Cheng. Dietary Flavonoids Luteolin and Quercetin Inhibit Migration and Invasion of Squamous Carcinoma through Reduction of Src/Stat3/S100A7 Signaling. Antioxidants. 2019; 8 (11):557.
Chicago/Turabian StyleJhen-Jia Fan; Wen-Hsien Hsu; Kuen-Haur Lee; Ku-Chung Chen; Cheng-Wei Lin; Yu-Lin A Lee; Tzu-Ping Ko; Lang-Ta Lee; Ming-Ting Lee; Mau-Sun Chang; Chia-Hsiung Cheng. 2019. "Dietary Flavonoids Luteolin and Quercetin Inhibit Migration and Invasion of Squamous Carcinoma through Reduction of Src/Stat3/S100A7 Signaling." Antioxidants 8, no. 11: 557.
The polyprenoid glycan carriers are produced by cis-prenyltransferases (cis-PTs), which function as heterodimers in metazoa and fungi or homodimers in bacteria, but both are found in plants, protista and archaea. Heterodimeric cis-PTs comprise catalytic and non-catalytic subunits while homodimeric enzymes contain two catalytic subunits. The non-catalytic subunits of cis-PT shows low sequence similarity to known cis-PTs and their structure information is of great interests. Here we report the crystal structure of Nus1, the non-catalytic subunit of cis-PT from Saccharomyces cerevisiae. We also investigate the heterodimer formation and active site conformation by constructing a homology model of Nus1 and its catalytic subunit. Nus1 does not contain an active site, but its C-terminus may participate in catalysis by interacting with the substrates bound to the catalytic subunit. These results provide important basis for further investigation of heterodimeric cis-PTs.
Jiantao Ma; Tzu-Ping Ko; Xuejing Yu; Lilan Zhang; Lixin Ma; Chao Zhai; Rey-Ting Guo; Weidong Liu; Huazhong Li; Chun-Chi Chen. Structural insights to heterodimeric cis-prenyltransferases through yeast dehydrodolichyl diphosphate synthase subunit Nus1. Biochemical and Biophysical Research Communications 2019, 515, 621 -626.
AMA StyleJiantao Ma, Tzu-Ping Ko, Xuejing Yu, Lilan Zhang, Lixin Ma, Chao Zhai, Rey-Ting Guo, Weidong Liu, Huazhong Li, Chun-Chi Chen. Structural insights to heterodimeric cis-prenyltransferases through yeast dehydrodolichyl diphosphate synthase subunit Nus1. Biochemical and Biophysical Research Communications. 2019; 515 (4):621-626.
Chicago/Turabian StyleJiantao Ma; Tzu-Ping Ko; Xuejing Yu; Lilan Zhang; Lixin Ma; Chao Zhai; Rey-Ting Guo; Weidong Liu; Huazhong Li; Chun-Chi Chen. 2019. "Structural insights to heterodimeric cis-prenyltransferases through yeast dehydrodolichyl diphosphate synthase subunit Nus1." Biochemical and Biophysical Research Communications 515, no. 4: 621-626.
Recent research on the structure and mechanism of DNA polymerases has continued to generate fundamentally important features, including a noncanonical pathway involving "prebinding" of metal-bound dNTP (MdNTP) in the absence of DNA. While this noncanonical mechanism was shown to be a possible subset for African swine fever DNA polymerase X (Pol X) and human Pol λ, it remains unknown whether it could be the primary pathway for a DNA polymerase. Pol μ is a unique member of the X-family with multiple functions and with unusual Mn2+ preference. Here we report that Pol μ not only prebinds MdNTP in a catalytically active conformation but also exerts a Mn2+ over Mg2+ preference at this early stage of catalysis, for various functions: incorporation of dNTP into a single nucleotide gapped DNA, incorporation of rNTP in the nonhomologous end joining (NHEJ) repair, incorporation of dNTP to an ssDNA, and incorporation of an 8-oxo-dGTP opposite template dA (mismatched) or dC (matched). The structural basis of this noncanonical mechanism and Mn2+ over Mg2+ preference in these functions was analyzed by solving 19 structures of prebinding binary complexes, precatalytic ternary complexes, and product complexes. The results suggest that the noncanonical pathway is functionally relevant for the multiple functions of Pol μ. Overall, this work provides the structural and mechanistic basis for the long-standing puzzle in the Mn2+ preference of Pol μ and expands the landscape of the possible mechanisms of DNA polymerases to include both mechanistic pathways.
Yao-Kai Chang; Ya-Ping Huang; Xiao-Xia Liu; Tzu-Ping Ko; Yoshitaka Bessho; Yoshiaki Kawano; Manuel Maestre-Reyna; Wen-Jin Wu; Ming-Daw Tsai. Human DNA Polymerase μ Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions. Journal of the American Chemical Society 2019, 141, 8489 -8502.
AMA StyleYao-Kai Chang, Ya-Ping Huang, Xiao-Xia Liu, Tzu-Ping Ko, Yoshitaka Bessho, Yoshiaki Kawano, Manuel Maestre-Reyna, Wen-Jin Wu, Ming-Daw Tsai. Human DNA Polymerase μ Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions. Journal of the American Chemical Society. 2019; 141 (21):8489-8502.
Chicago/Turabian StyleYao-Kai Chang; Ya-Ping Huang; Xiao-Xia Liu; Tzu-Ping Ko; Yoshitaka Bessho; Yoshiaki Kawano; Manuel Maestre-Reyna; Wen-Jin Wu; Ming-Daw Tsai. 2019. "Human DNA Polymerase μ Can Use a Noncanonical Mechanism for Multiple Mn2+-Mediated Functions." Journal of the American Chemical Society 141, no. 21: 8489-8502.
Crystal structure of a calcium-depleted Stig cyclase revealing the mechanism of metal-dependence of enzyme activity.
Xueke Tang; Jing Xue; Yunyun Yang; Tzu-Ping Ko; Chin-Yu Chen; Longhai Dai; Rey-Ting Guo; Yonghui Zhang; Chun-Chi Chen. Structural insights into the calcium dependence of Stig cyclases. RSC Advances 2019, 9, 13182 -13185.
AMA StyleXueke Tang, Jing Xue, Yunyun Yang, Tzu-Ping Ko, Chin-Yu Chen, Longhai Dai, Rey-Ting Guo, Yonghui Zhang, Chun-Chi Chen. Structural insights into the calcium dependence of Stig cyclases. RSC Advances. 2019; 9 (23):13182-13185.
Chicago/Turabian StyleXueke Tang; Jing Xue; Yunyun Yang; Tzu-Ping Ko; Chin-Yu Chen; Longhai Dai; Rey-Ting Guo; Yonghui Zhang; Chun-Chi Chen. 2019. "Structural insights into the calcium dependence of Stig cyclases." RSC Advances 9, no. 23: 13182-13185.
Acute hepatopancreatic necrosis disease (AHPND) is a newly emergent penaeid shrimp disease which can cause 70–100% mortality in Penaeus vannamei and Penaeus monodon, and has resulted in enormous economic losses since its appearance. AHPND is caused by the specific strains of Vibrio parahaemolyticus that harbor the pVA1 plasmid and express PirAvp and PirBvp toxins. These two toxins have been reported to form a binary complex. When both are present, they lead to the death of shrimp epithelial cells in the hepatopancreas and cause the typical histological symptoms of AHPND. However, the binding mode of PirAvp and PirBvp has not yet been determined. Here, we used isothermal titration calorimetry (ITC) to measure the binding affinity of PirAvp and PirBvp. Since the dissociation constant (Kd = 7.33 ± 1.20 μM) was considered too low to form a sufficiently stable complex for X-ray crystallographic analysis, we used alternative methods to investigate PirAvp-PirBvp interaction, first by using gel filtration to evaluate the molecular weight of the PirAvp/PirBvp complex, and then by using cross-linking and hydrogen-deuterium exchange (HDX) mass spectrometry to further understand the interaction interface between PirAvp and PirBvp. Based on these results, we propose a heterotetrameric interaction model of this binary toxin complex. This model provides insight of how conformational changes might activate the PirBvp N-terminal pore-forming domain and should be helpful for devising effective anti-AHPND strategies in the future.
Shin-Jen Lin; Yi-Fan Chen; Kai-Cheng Hsu; Yun-Ling Chen; Tzu-Ping Ko; Chu-Fang Lo; Han-Ching Wang. Structural Insights to the Heterotetrameric Interaction between the Vibrio parahaemolyticus PirAvp and PirBvp Toxins and Activation of the Cry-Like Pore-Forming Domain. Toxins 2019, 11, 233 .
AMA StyleShin-Jen Lin, Yi-Fan Chen, Kai-Cheng Hsu, Yun-Ling Chen, Tzu-Ping Ko, Chu-Fang Lo, Han-Ching Wang. Structural Insights to the Heterotetrameric Interaction between the Vibrio parahaemolyticus PirAvp and PirBvp Toxins and Activation of the Cry-Like Pore-Forming Domain. Toxins. 2019; 11 (4):233.
Chicago/Turabian StyleShin-Jen Lin; Yi-Fan Chen; Kai-Cheng Hsu; Yun-Ling Chen; Tzu-Ping Ko; Chu-Fang Lo; Han-Ching Wang. 2019. "Structural Insights to the Heterotetrameric Interaction between the Vibrio parahaemolyticus PirAvp and PirBvp Toxins and Activation of the Cry-Like Pore-Forming Domain." Toxins 11, no. 4: 233.
While cryo-EM is revolutionizing structural biology, its impact on enzymology is yet to be fully demonstrated. The ketol-acid reductoisomerase (KARI) catalyzes conversion of (2S)-acetolactate or (2S)-aceto-2-hydroxybutyrate to 2,3-dihydroxy-3-alkylbutyrate. We found that KARI from archaea Sulfolobus solfataricus (Sso-KARI) is unusual in being a dodecamer, bi-specific to NADH and NADPH, and losing activity above pH 7.8. While crystals were obtainable only at pH 8.5, cryo-EM structures were solved at pH 7.5 and 8.5 for Sso-KARI:2Mg2+. The results showed that the distances of the two catalytic Mg2+ ions are lengthened in both structures at pH 8.5. We next solved cryo-EM structures of two Sso-KARI complexes, with NADH+inhibitor and NADPH+inhibitor at pH 7.5, which indi-cate that the bi-specificity can be attributed to a unique aspara-gine at the cofactor binding loop. Unexpectedly, Sso-KARI also differs from other KARI enzymes in lacking “induced-fit”, reflecting structural rigidity. Thus, cryo-EM is powerful for structural and mechanistic enzymology.
Chin-Yu Chen; Yuan-Chih Chang; Bo-Lin Lin; Kuan-Fu Lin; Chun-Hsiang Huang; Dong-Lin Hsieh; Tzu-Ping Ko; Ming-Daw Tsai. Use of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase. Journal of the American Chemical Society 2019, 141, 6136 -6140.
AMA StyleChin-Yu Chen, Yuan-Chih Chang, Bo-Lin Lin, Kuan-Fu Lin, Chun-Hsiang Huang, Dong-Lin Hsieh, Tzu-Ping Ko, Ming-Daw Tsai. Use of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase. Journal of the American Chemical Society. 2019; 141 (15):6136-6140.
Chicago/Turabian StyleChin-Yu Chen; Yuan-Chih Chang; Bo-Lin Lin; Kuan-Fu Lin; Chun-Hsiang Huang; Dong-Lin Hsieh; Tzu-Ping Ko; Ming-Daw Tsai. 2019. "Use of Cryo-EM To Uncover Structural Bases of pH Effect and Cofactor Bispecificity of Ketol-Acid Reductoisomerase." Journal of the American Chemical Society 141, no. 15: 6136-6140.
Decaprenyl diphosphate synthase from Mycobacterium tuberculosis (MtDPPS, also known as Rv2361c) catalyzes the consecutive elongation of ω,E,Z-farnesyl diphosphate (EZ-FPP) by seven isoprene units by forming new cis double bonds. The protein folds into a butterfly-like homodimer like most other cis-type prenyltransferases. The starting allylic substrate EZ-FPP is bound to the S1 site and the homoallylic substrate to be incorporated, isopentenyl diphosphate, is bound to the S2 site. Here, a 1.55 Å resolution structure of MtDPPS in complex with the substrate analogues geranyl S-thiodiphosphate (GSPP) and isopentenyl S-thiodiphosphate bound to their respective sites in one subunit clearly shows the active-site configuration and the magnesium-coordinated geometry for catalysis. The ligand-binding mode of GSPP in the other subunit indicates a possible pathway of product translocation from the S2 site to the S1 site, as required for the next step of the reaction. The preferred binding of negatively charged effectors to the S1 site also suggests a promising direction for inhibitor design.
Tzu-Ping Ko; Xiansha Xiao; Rey-Ting Guo; Jian-Wen Huang; Weidong Liu; Chun-Chi Chen. Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase. Acta Crystallographica Section F Structural Biology Communications 2019, 75, 212 -216.
AMA StyleTzu-Ping Ko, Xiansha Xiao, Rey-Ting Guo, Jian-Wen Huang, Weidong Liu, Chun-Chi Chen. Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase. Acta Crystallographica Section F Structural Biology Communications. 2019; 75 (4):212-216.
Chicago/Turabian StyleTzu-Ping Ko; Xiansha Xiao; Rey-Ting Guo; Jian-Wen Huang; Weidong Liu; Chun-Chi Chen. 2019. "Substrate-analogue complex structure of Mycobacterium tuberculosis decaprenyl diphosphate synthase." Acta Crystallographica Section F Structural Biology Communications 75, no. 4: 212-216.
Chromoproteins are a good source of engineered biological tools. We previously reported the development of a blue fluorescent protein, termed shBFP, which was derived from a purple chromoprotein shCP found in the sea anemone Stichodacyla haddoni. shBFP contains a Leu63-Leu64-Gly65 tri-peptide chromophore, and shows maximum excitation and emission wavelengths at 401 nm and 458 nm, along with a high quantum yield. How this chromophore endows shBFP with the unique fluorescence property in the absence of a hydroxyphenyl ring remained unclear. Here, we present the crystal structures of shCP and shBFP at 1.9- and 2.05-Å resolution, respectively. Both proteins crystallized as similar tetramers, but they are more likely to function as dimers in solution. The chromophore in shCP shows a trans-conformation and its non-planarity is similar to most other homologues. The shBFP chromophore also contains an imidazolidone moiety in its structure, but there are a smaller number of conjugated double bonds compared to shCP. Consequently, the chromophore may prefer absorbing shorter wavelength lights in the UV region, followed by the emission of blue fluorescence. These observations provide new insights into the molecular basis that correlates chromophore conformation with light absorption and fluorescence emission for the development of improved biomarkers.
Hsin-Yang Chang; Tzu-Ping Ko; Yu-Ching Chang; Kai-Fa Huang; Cheng-Yung Lin; Hong-Yun Chou; Cheng-Yi Chiang; Huai-Jen Tsai. Crystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide chromophore derived from the purple chromoprotein of Stichodactyla haddoni. International Journal of Biological Macromolecules 2019, 130, 675 -684.
AMA StyleHsin-Yang Chang, Tzu-Ping Ko, Yu-Ching Chang, Kai-Fa Huang, Cheng-Yung Lin, Hong-Yun Chou, Cheng-Yi Chiang, Huai-Jen Tsai. Crystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide chromophore derived from the purple chromoprotein of Stichodactyla haddoni. International Journal of Biological Macromolecules. 2019; 130 ():675-684.
Chicago/Turabian StyleHsin-Yang Chang; Tzu-Ping Ko; Yu-Ching Chang; Kai-Fa Huang; Cheng-Yung Lin; Hong-Yun Chou; Cheng-Yi Chiang; Huai-Jen Tsai. 2019. "Crystal structure of the blue fluorescent protein with a Leu-Leu-Gly tri-peptide chromophore derived from the purple chromoprotein of Stichodactyla haddoni." International Journal of Biological Macromolecules 130, no. : 675-684.
Crystal structure of LepI, a SAM-dependent enzyme which can catalyze seteroselective dehydration, Diels–Alder reaction, and retro-Claisen rearrangement.
Zhenying Chang; Tamar Ansbacher; Lilan Zhang; Yong Yang; Tzu-Ping Ko; Guimin Zhang; Weidong Liu; Jian-Wen Huang; Longhai Dai; Rey-Ting Guo; Dan Thomas Major; Chun-Chi Chen; Zhenyin Chang. Crystal structure of LepI, a multifunctional SAM-dependent enzyme which catalyzes pericyclic reactions in leporin biosynthesis. Organic & Biomolecular Chemistry 2019, 17, 2070 -2076.
AMA StyleZhenying Chang, Tamar Ansbacher, Lilan Zhang, Yong Yang, Tzu-Ping Ko, Guimin Zhang, Weidong Liu, Jian-Wen Huang, Longhai Dai, Rey-Ting Guo, Dan Thomas Major, Chun-Chi Chen, Zhenyin Chang. Crystal structure of LepI, a multifunctional SAM-dependent enzyme which catalyzes pericyclic reactions in leporin biosynthesis. Organic & Biomolecular Chemistry. 2019; 17 (8):2070-2076.
Chicago/Turabian StyleZhenying Chang; Tamar Ansbacher; Lilan Zhang; Yong Yang; Tzu-Ping Ko; Guimin Zhang; Weidong Liu; Jian-Wen Huang; Longhai Dai; Rey-Ting Guo; Dan Thomas Major; Chun-Chi Chen; Zhenyin Chang. 2019. "Crystal structure of LepI, a multifunctional SAM-dependent enzyme which catalyzes pericyclic reactions in leporin biosynthesis." Organic & Biomolecular Chemistry 17, no. 8: 2070-2076.
Undecaprenyl pyrophosphate (UPP) is an important carrier of the oligosaccharide component in peptidoglycan synthesis. Inhibition of UPP synthase (UPPS) may be an effective strategy in combating the pathogen Acinetobacter baumannii, which has evolved to be multidrug-resistant. Here, A. baumannii UPPS (AbUPPS) was cloned, expressed, purified and crystallized, and its structure was determined by X-ray diffraction. Each chain of the dimeric protein folds into a central β-sheet with several surrounding α-helices, including one at the C-terminus. In the active site, two molecules of citrate interact with the side chains of the catalytic aspartate and serine. These observations may provide a structural basis for inhibitor design against AbUPPS.
Tzu-Ping Ko; Chi-Hung Huang; Shu-Jung Lai; Yeh Chen. Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallographica Section F Structural Biology Communications 2018, 74, 765 -769.
AMA StyleTzu-Ping Ko, Chi-Hung Huang, Shu-Jung Lai, Yeh Chen. Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii. Acta Crystallographica Section F Structural Biology Communications. 2018; 74 (12):765-769.
Chicago/Turabian StyleTzu-Ping Ko; Chi-Hung Huang; Shu-Jung Lai; Yeh Chen. 2018. "Structure of undecaprenyl pyrophosphate synthase from Acinetobacter baumannii." Acta Crystallographica Section F Structural Biology Communications 74, no. 12: 765-769.
Chun-Chi Chen; Xiangying Hu; Xueke Tang; Yunyun Yang; Tzu-Ping Ko; Jian Gao; Yingying Zheng; Jian-Wen Huang; Zhengsen Yu; Liping Li; Shuai Han; Ningning Cai; Yonghui Zhang; Weidong Liu; Rey-Ting Guo. Back Cover: The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement (Angew. Chem. Int. Ed. 46/2018). Angewandte Chemie International Edition 2018, 57, 15284 -15284.
AMA StyleChun-Chi Chen, Xiangying Hu, Xueke Tang, Yunyun Yang, Tzu-Ping Ko, Jian Gao, Yingying Zheng, Jian-Wen Huang, Zhengsen Yu, Liping Li, Shuai Han, Ningning Cai, Yonghui Zhang, Weidong Liu, Rey-Ting Guo. Back Cover: The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement (Angew. Chem. Int. Ed. 46/2018). Angewandte Chemie International Edition. 2018; 57 (46):15284-15284.
Chicago/Turabian StyleChun-Chi Chen; Xiangying Hu; Xueke Tang; Yunyun Yang; Tzu-Ping Ko; Jian Gao; Yingying Zheng; Jian-Wen Huang; Zhengsen Yu; Liping Li; Shuai Han; Ningning Cai; Yonghui Zhang; Weidong Liu; Rey-Ting Guo. 2018. "Back Cover: The Crystal Structure of a Class of Cyclases that Catalyze the Cope Rearrangement (Angew. Chem. Int. Ed. 46/2018)." Angewandte Chemie International Edition 57, no. 46: 15284-15284.