Publications

2020

Wu*, C.C., Lin*, J.L.J. and Yuan*, H. S. 

Structures, mechanisms and functions of His-Me finger nucleases.

Trends Biochem. Sci. (2020).

Lin, C.-C., Chen, Y. P., Yang, W. Z., Shen, J.C.K., and Yuan*, H. S
Structural insights into CpG-specific DNA methylation by human DNA methyltransferase 3B
Nucleic Acids Res.. 48, 3949-3961 (2020).

2019

Wu, C.C., Lin, J.L.J., Yang-Yen, H.-F. and Yuan*, H. S. 
A unique exonuclease ExoG cleaves at the junction between RNA and DNA in mitochondrial DNA replication. 
Nucleic Acids Res. 47, 5405-5419 (2019).

Chu, L.-Y., Agrawal, S., Chen, Y. P., Yang, W. Z. and Yuan*, H. S. 
Structural insights into nanoRNA degradation by human Rexo2. 
RNA 25, 737-746 (2019).

Agrawal, S., Kuo, P.-H., Chu, L.-Y., Golzarroshan, B., Jain, M. and Yuan*, H. S. 
RNA recognition motifs of disease-linked RNA-binding proteins contribute to amyloid formation. 
Sci. Rep. 9, 6171 (2019).

2018

Golzarroshan, B., Lin, C.-L., Li, C.-L., W.-Z. Yang, Chu, L.-Y., Agrawal, S. and Yuan*, H. S.
Crystal structure of dimeric human PNPase reveals why disease-linked mutants suffer from low RNA import and degradation activities.
Nucleic Acids Res. 46, 8630-8640 (2018).

Li, C.-L., W.-Z. Yang, Shi, Z. and Yuan*, H. S.
Tudor staphylococcal nuclease is a structure-specific ribonuclease that degrades RNA at unstructured regions during microRNA decay.
RNA 24, 739-748 (2018).

2017

Chu, L.-Y., Hsieh, T.-J., Golzarroshan, B., Chen, Y.-P., Agrawal, S. and Yuan*, H. S.
Structural insights into RNase R in RNA unwinding and degradation.
Nucleic Acids Res. 45,12015–12024(2017).

Huen, J., Lin, C.-L., Yi, W.-L., W.-Z. Yang, Golzarroshan, B. and Yuan*, H. S.
Structural insights into a unique dimeric DEAD-box helicase CshA that promotes RNA decay.
Structure 25, 469–481 (2017).

2016

Lin, J. L. J., Wu, C.-C., Yang, W.-Z. and and Yuan*, H. S.
Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer.
Nucleic Acids Res. 44,10480-10490 (2016).

Huang, K.-W., Hsu, K.-C., Chu, L.-Y., Yang, J.-M. Yuan*, H. S. and Hsiao*, Y.-Y.
Identification of inhibitors for the DEDDh family of exonucleases and a unique inhibition mechanism revealed by crystal structure analysis of CRN-4 bound with 2-morpholin-4-ylethanesulfonate (MES).
J. Med. Chem. 59(17):8019-29 (2016).

Lin, J. L. J., Nakagawa, A., Skeen-Gaar, R. Yang, W.-Z., X., Ge, S., Mitani, Xue*, D. and Yuan*, H. S.
Oxidative stress impairs cell death by repressing the nuclease activity of Endonuclease G.
Cell Rep.12, 279-287 (2016).

Zhou, Q., Li, H., Li, H., Nakagawa, A., Lin, J. L. J., Lee, E.-S., Harry, B.L., Skleen-Gaar, R., Shehiro, Y., William, D., Mitani, S., Yuan, H. S., Kang*, B.-H., Xue*, D.
Mitochondrial endonuclease G mediates breakdown of paternal mitochondria upon fertilization.
Science  353, 394-399 (2016).

Lee, Y.-M., Duh, Y., Wang, S.-T., Lai*, M.M.C., Yuan*, H. S. and Lim*, C.
Using an old drug to target a new drug site: Application of disulfiram to target the Zn-site in HCV NS5A protein.
J. Am. Chem. Soc. 138, 3856-62 (2016).

Chiang, C. -H., Grauffel, C. Wu, L.-S., Kuo, P.-H., Doudeva, L. G, Lim, C., Shen, C.K.J. and Yuan*, H. S.
Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation.

Sci. Rep. 6: 21581 (2016).

2015

Duh, Y., Hsiao, Y.-Y., Li, C.-L., Huang, J. C. and  Yuan*, H. S.
Aromatic residues in RNase T stack with nucleobases to guide  the sequence-specific recognition and cleavage of nucleic acids.
Protein Sci. 24, 1934-1941 (2015).

2014

Hsiao, Y.-Y., Fang, W.-H., Lee, C.-C, Chen, Y.-P., Hsu, P.-C. and Yuan*, H. S. 
Structural insights into DNA repair by RNase T, an exonuclease processing 3′ end of structured DNA in repair pathways.
PLoS Biol. 12, 3, e1001803 (2014).

Kuo, P.-H, Chiang, C.-H, Wang, Y.-T., Doudeva, L. G., and Yuan*, H. S.  
The crystal structure of TDP-43 RRM1-DNA complex reveals the specific recognition for UG- and TG-rich nucleic acids.
Nucleic Acids Res. 42, 4712-4722 (2014).

Chen, Y.-J., Li, C.-L., Hsiao, Y.-Y., Duh, Y. and Yuan*, H. S.
Structure and function of TatD exonuclease in DNA repair.
Nucleic Acids Res.10776-10785 (2014).

Fang, Y.-S., Chang, Y.-J., Kuo, P.-H., Tsai, K.-J., Liao, J.Y., Chou, S,-C, Lin V., Yuan, H. S., Cheng, I. H, Tu, P.-H., and Chen*,Y.-R.
Full-length TDP-43 forms toxic amyloid oligomers that are present in frontotemporal lobar dementia-TDP patients.
Nature Comm., 5, 4824 (2014).

2013

Lee, Y.-M., Wang, Y.-T., Duh, Y., Yuan*, H. S. and Lim*, C.  
Identification of labile Zn sites in drug-target proteins.
J. Am. Chem. Soc. 2013, 135, 4028-4031 (2013).  

Wang, Y. -T., Kuo, P. -H., Chiang, C. -H, Liang., J -R., Chen, Y. -R., Wang, S., Shen, J.C.K., and Yuan*, H. S.
The truncated C-terminal RNA recognition motif of TDP-43 protein plays a key role in forming proteinaceous aggregates.
J. Biol. Chem. 2013, 288, 13, 9049–9057 (2013).

2012

Su. M. W., Yuan, S. H. and W. C. Chu* 
Recombination in the non-structural gene region in type-2 dengue viruses.
Intervirol. 2012, 55, 225-230 (2012).

Hsiao, Y.-Y., Duh, Y., Chen, Y.-P., Wang, Y.-T., and Yuan*, H. S.
How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T-product complexes.
Nucleic Acids Res. 40, 8144-8154 (2012).

Lin, J. L. J., Lin, C. L., Hsiao, Y. Y., Doudeva, L. G., Yang, W.-Z., Wang, Y.-T. and Yuan*, H. S. 
Structural insights into DNA binding and cleavage by CED-3 Protease Suppressor-6 (CPS-6) from Caenorhabditis elegans.
J. Biol. Chem. 287, 10, 7110-7120 (2012).
 
Lin C. L., Wang, Y.-T, Hsiao, Y.-Y., Yang, W.-Z. and Yuan*, H. S. 
Crystal structure of human polynucleotide phosphorylase: Insights into its domain function in RNA binding and degradation.
Nucleic Acids Res. 40, 4146-4157(2012).

2011

Hsiao, Y.-Y., Yang, C.-C, Lin C. L., Lin, J. L. J., Duh, Y. and Yuan*, H. S.
Structural basis for RNA trimming by RNase T in stable RNA 3'-end maturation.
Nature Chem. Biol. 7, 236-243(2012).

2010

Yang, C.-C, Wang, Y.-T., Hsiao, Y. Y., Doudeva, L. G., Kuo, P.-H., Chow, S. Y. and Yuan*, H. S.
Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation.
RNA 16: 1748-1759 (2010).

Fu, C. C., Lin, C. F., Gao, Q. Z., Yang, W. Z., Lim, T. S., Yang, L. L, Yen, C. F., Chang, W. H., Yuan, H. S., Sheu*, S. Y., Yang*, D. Y., Fann, W. 
Fis-protein induces rod-like DNA bending.
Chem. Phys. Letter 500, 318-322 (2010).

2009

Su, M.-W., Lin, H.-M., Yuan*, H. S. and Chu*, W.-C
Categorizing host-dependent RNA viruses by principal component analysis of their coden usage preferences.
J. Comp. Biol. 16, 1539-1547 (2009).

Wang, Y.-T., Wright, J, D., Doudeva, L. G., H -C., Lim*, C. and Yuan*, H. S. 
Redesign of high-affinity nonspecifid nucleases with altered sequence preference.
J. Am. Chem. Soc. 2009, 131, 17345-17353 (2009).

Hsiao, Y. Y., Nakagawa, A., Shi, Z., Mitani, S., Xue, D. and Yuan*, H. S. 
Crystal structure of CRN-4: implications for domain function in apoptotic DNA degradation. 
Mol. Cell. Biol. 29, 2, 448-457 (2009).
 
Lin, Y.-S., Tsai; L.-C., Lee, S.-H., Yuan, H. S. and Shyur*, L.-F.
Structural and catalytic roles of residues located in beta13 strand and the following beta-turn loop in Fibrobacter succinogenes 1,3-1,4- beta -D-glucanase.
Biochim. Biophys. Acta. 1790, 231–239 (2009).

Kuo, P,-S, Doudeva, L. G., Wang, Y.-T., Shen, C.-K. J. and Yuan*, H. S. 
Structural insights into TDP-43 in nucleic acid binding and domain interactions. 
Nucleic Acids Res. 37, 6, 1799-1808 (2009). 

2008

Shi, Z., Yang, W.-Z., Lin-Chao, S., Chak, K.-F. and Yuan*, H. S. 
Crystal structure of Escherichia coli PNPase: central channel residues are involved in processive RNA degradation.
RNA 14, 1-11 (2008).

Li, C. -L.,Yang, W. -Z., Chen, Y. -P. and Yuan*, H. S.
Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing.
Nucleic Acid Res. 36, 11, 3579-3589 (2008).
 
2007
 
Lei, G. -S., Chen, C. -J., Yuan, H. S., Wang., S. -H. and Hu*, S. -T.
Inhibition of IS2 transposition by factor for inversion stimulation. 
FEMS Microbiol Lett. 275, 98-105 (2007).
 
Huang, H. and Yuan*, H. S.  
The conserved asparagine in the HNH motif plays an important structural role in metal finger endonucleases.  
J. Mol. Biol. 368, 3, 812-821 (2007).
 
Wang, Y. -T., Yang, Y. -J., Li, C. -L., Doudeva, L. G., and Yuan*, H. S.
Structural basis for sequence-dependent DNA cleavage by nonspecific endonucleases.
Nucleic Acid Res. 35, 2, 584-594 (2007).
 
2006
　
Pan, Y. -H., Liao, C. -C., Kuo, C. -C., Duan, K.-J., Liang, P.-H, Yuan, H. S., Hu, S.-T. and Chak*, K.-F. 
The critical roles of polyamines in regulating ColE7 production and restricting ColE7 uptake of the colicin-producing Escherichia coli.
J. Biol. Chem.  281, 13083 (2006).
　
Doudeva, L. G., Huang, H., Hsia, K.-C., Shi, Z., Li, C. -L., Cheng, Y. -S. and Yuan*, H. S.
Crystal structural analysis and metal-dependent stability and activity studies of the ColE7 endonuclease domain in complex with DNA/Zn²⁺ or inhibitor/Ni²⁺.
Protein Sci. 15, 269-280 (2006).
　
Cheng, Y.-S., Shi, Z., Doudeva, L. G., Yang, W. -Z., Chak, K. -F. and Yuan*, H. S.
High-resolution crystal structure of a truncated ColE7 translocation domain: Implications for colicin transport across membranes. 
J. Mol. Biol. 356, 22-31 (2006).
　
2005
　
Hsia, K.-C., Li, C. -L. and Yuan*, H. S.
Structural and functional insight into the sugar-nonspecific nucleases in host defense.
Curr. Opin. Struct. Biol. 15, 126-134 (2005).

Liu, H., Peng, H.-W., Cheng, Y.-S., Yuan, H. S. and Yang-Yen*, H.-F.
Stabilization and enhancement of the antiapoptotic activity of Mcl-1 by TCTP. 
Mol. Cell. Biol. 3117–3126 (2005).
 
Shi, Z., Chak. K.-F. and Yuan*, H. S.
Identification of an essential cleavage site in ColE7 required for import and killing of cells. 
J. Biol. Chem. 2005, 280, 24663-24668 (2005).
　 　
2004
 
Hsia, K.-C., Chak, K.-F., Liang, P. -H., Cheng, Y. -S., Ku, W. -Y. and Yuan*, H. S. 
DNA binding and degradation by the H-N-H protein ColE7
Structure 12, 205-214 (2004).
 
Lin, Y.-H., Liao, C. -C., Liang, P. -H., Yuan*, H. S. and Chak*, K. -F.
Involvement of colicin in the limited protection of the colicin producing cells against bacteriophage
Biochem. Biophys. Res. Commun. 318, 81-87 (2004).
 
2003
 
Tsai, L. -C., Shyur, L. -F., Lee, S. -H., Lin, S. -S. and Yuan*, H. S. 
Crystal structure of a natural circularly-permutated jellyroll protein: 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes.
J. Mol. Biol. 330, 607-620 (2003).
 
Li, C. -L., Hor, L. -I., Chang, Z. -F., Tsai, L. -C., Yang, W. -Z. and Yuan*, H. S. 
DNA binding and cleavage by the periplasmic nuclease Vvn- A novel structure with a known active site.
EMBO J. 22, 4014-4025 (2003).
 
2002
　
Chang, S. -J., Hsieh, S. -Y., Yuan, H. S. and Chak*, K.-F. 
Characterization of the specific cleavage of ceiE7-mRNA of the bactericidal ColE7 operon.
Biochem. Biophys. Res. Commun. 299, 613-620 (2002).

Cheng, Y. -S., Hsia, K. -C., Doudeva, L. G., Kin-Fu Chak and Yuan*, H. S.
The crystal structure of the nuclease domain of colicin E7 suggests a mechanism for binding to double-stranded DNA by the H-N-H endonucleases.
J. Mol. Biol. 324, 227-236 (2002).
　
Sui, M. -J., Tsai, L. -C., Hsia, K. -C., Doudeva, L. G., Ku, W.-Y., Han, G. W. and Yuan*, H. S.
Metal ions and phosphate binding in the H-N-H motif: Crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions. 
Protein Sci. 11, 2947-2957 (2002).
　
Cheng, H. -L., Tsai, L. -C., Lin, S. -S., Yuan*, H. S., Yang, N. -S., Lee, S. -H. and Shyur*, L. -F.
Mutagenesis of Trp54 and Trp203 residues on Fibrobacter Succinogens 1,3-1,4-b-D-glucanase significantly affects catalytic activities of the enzyme. 
Biochemistry 2002, 41, 8759-8766 (2002).
　
Ku, W. -Y., Liu, Y. -W., Hsu, Y. -C., Liao, C. -C., Liang, P. -H., Yuan, H. S. and Chak*, K. -F. 
The zinc ion in the HNH motif of the endonuclease domain of colicin E7 is not required for DNA binding but is essential for DNA hydrolysis.
Nucleic Acid Res. 30, 1670-1678 (2002).
　
Yang Z., Zhang H., Hung, H. -C., Kuo, C. -C., Tsai, L. -C., Yuan, H. S., Chou, W. -Y., Chang, G. -G., Tong*, L. 
Structural studies of the pigeon cytosolic NADP(+)-dependent malic enzyme. 
Protein Sci. 11:332-41 (2002).

2001

Chen, J. L., Tsai, L. C., Wen, T. N., Tang, J. B., Yuan*, H. S. and Shyur*, L. F.
Directed mutagenesis of specific active site residues on Fibrobacter succinogenes 1,3-1,4-beta-D-glucanase significantly affects catalysis and enzyme structural stability.
J. Biol. Chem. 276, 17895-17901 (2001).

Tsai, L. C., Shyur, L. F., Lin, S. S., Yuan*, H. S.
Crystallization and preliminary X-ray diffraction analysis of the 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes.
Acta Cryst. D. 57, 1303-1306 (2001).
　
2000
　
Cheng, Y.-S., Yang, W.-Z., Johnson, R. C. and Yuan*, H. S.
Structure analysis of the transcriptional activation region on Fis: Crystal structures of Six Fis Mutants with Different activation properties.  
J. Mol. Biol. 302, 1139-1151 (2000).
 
1999

Ko, T.-P., Liao, C.-C., Ku, W.-Y., Chak, K.-F. and Yuan*, H. S.
The crystal structure of the DNase domain of colicin E7 in complex with its inhibitor Im7 protein.
Structure 7, 91-102 (1999).
 
Tsai, L.-C, Kuo, C.-C., Chou, W.-Y., Chang, G.-G. and Yuan*, H. S.
Crystallization and preliminary x-ray diffraction analysis of malic enzyme from pigeon liver.
Acta Cryst. D. 55, 1930-1932 (1999).
 
Ko, T.-P., Yang, W.-Z, Wu, S.-P., Hsin, T., and Yuan*, H. S.
The preliminary crystallographic analysis of the open-form E. coli tyrosine aminotransfer ase bound with a cofactor pyridoxal 5'-phosphate.
Acta Cryst. D. 55, 1474-1477 (1999). 
 
Lu, F.-M., Yuan*, H. S., Hsu, Y.-C., Chang, S.-J., Chak*, K.-F. 
Hierarchical order of critical residues on the immunity-determining region of the Im7 protein which confer specific immunity to its cognate colicin.
Biochem. Biophys. Res. Commun. 264, 69-75 (1999).
　
Chang*, S.-L., Chao, C.-H., Huang, Y.-S., Jean, Y.-C., Sheu, H.-S., Liang, F.-J., Chen, C.-K., Yuan*, H. S.
Quantitative phase determination for macromolecular crystals using stereoscopic multibeam imaging
Acta. Cryst. A. 55, 933-938 (1999). 
 
Hsu, W.-H., Chien, F.-T., Hsu, C.-L., Wang, T.-C., Yuan*, H. S., and Wang*, W.-C.
Expression, crystallization and preliminary x-ray diffraction studies of N- carbamyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter.
Acta. Cryst. D. 55, 694-695 (1999). 
 
1998
 
Yang, W.-Z, Ko, T. P., Corselli, L., Johnson, R. C. and Yuan*, H. S.
The conversion from a beta-strand to an alph-helix induced by a single-site mutation identified in the crystal structures of Fis mutant Pro26Ala.
Protein Sci. 7, 1875-1883 (1998).
 
1997
 
Safo, M. K., Yang, W.-Z., Corselli, L., Crampton, S., Yuan*, H. S, and Johnson*, R. C.
The transactivation region of the Fis protein that controls site-specific DNA inversion contains extended mobile beta-hairpin arms.
EMBO J. 16, 6860-6873 (1997).
 
Hsieh, S. -H., Ko, T. -P., Tseng, M. -Y., Ku, W. -Y., Chak*, K.-F, and Yuan*, H. S.
A novel role of ImmE7 in the autoregulatory expression of ColE7 operon and identification of possible ribonuclease active sites in the crystal structure of dimeric ImmE7.
EMBO J. 16, 1444-1454 (1997).

1996
 
Chak, K.-F., Safo, M. K., Ku, W.-Y., Hsieh, S.-Y., and Yuan*, H. S.
The crystal structure of the ImmE7 protein suggests a possible colicin-interacting surface.
Proc. Natl. Acad. Sci. USA 93, 6437-6442 (1996).

1995
 
Ku, W. -Y., Wang, C. -S., Chen, J. -Y., Chak, K.-F., Safo, M. K. and Yuan*, H. S.
Crystallization and preliminary crystallographic analysis of ImmE7 protein of Colicin E7.
Proteins, Struc. Func. & Genet. 23, 588-590 (1995).
 
1994
 
Yuan*, H. S., Yang, W.-Z., Wang, S. S., Finkel, S. E. and Johnson, R. C.
The structure of Fis mutant Pro61-Ala illustrates that the kink within the long a-helix is not due to the presence of the proline residue. 
J. Biol. Chem. 269, 46, 28947-28954 (1994).
 
Yuan*, H. S., Stevens, R. C., Kotzle, T. F. and Bau*, R.
Determination of the absolute configuration of (S)-(+)-neopentyl-1-d alcohol by neutron diffraction study of strychnium neopentylphthalate.
Proc. Natl. Acad. Sci. USA 91, 12872-12876 (1994).