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Structure of human lysine methyltransferase Smyd2 reveals insights into the substrate divergence in Smyd proteins

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Journal of Molecular Cell Biology 2011年第5期3卷 293-300页

作者： Shutong Xu Chen Zhong Tianlong Zhang jianping ding State Key Laboratory of Molecular Biology and Research Center for Structural Biology Institute of Biochemistry and Cell BiologyShanghai Institutes for Biological SciencesChinese Academy of SciencesShanghai 200031China Graduate School of Chinese Academy of Sciences 320 YueYang RoadShanghai 200031China

The SET-and myeloid-Nervy-DEAF-1(MYND)-domain containing(Smyd)lysine methyltransferases 1–3 share relatively high sequence similarity but exhibit divergence in the substrate *** we report the crystal structure of the full-length human Smyd2 in complex with S-adenosyl-L-homocysteine(AdoHcy).Although the Smyd1–3 enzymes are similar in the overall structure,detailed comparisons demonstrate that they differ substantially in the potential substrate-binding *** binding site of Smyd3 consists mainly of a deep and narrow pocket,while those of Smyd1 and Smyd2 consist of a comparable pocket and a long *** addition,Smyd2,which has lysine methyltransferase activity on histone H3-lysine 36,exhibits substantial differences in the wall of the substrate-binding pocket compared with those of Smyd1 and Smyd3 which have activity specifically on histone H3-lysine *** differences in the substrate-binding site might account for the observed divergence in the specificity and methylation state of the *** modeling study of Smyd2 in complex with a p53 peptide indicates that mono-methylation of p53-Lys372 might result in steric conflict of the methyl group with the surrounding residues of Smyd2,providing a structural explanation for the inhibitory effect of the SET7/9-mediated mono-methylation of p53-Lys372 on the Smyd2-mediated methylation of p53-Lys370.

关键词： Smyd2 Smyd proteins SET family histone lysine methyltransferase epigenetics

Caenorhabditis elegans NMAD-1 functions as a demethylase for actin

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Journal of Molecular Cell Biology 2023年第1期15卷 62-65页

作者： Yu Shi Hui Yang jianping ding State Key Laboratory of Molecular Biology Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China School of Life Science Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China

Dear Editor,DNA N^(6)-methyladenine(6mA)modifi-cation,which was found in bacteria,archaea,viruses,and eukaryotes ranging from unicellular protists,fungi,and ciliates to multicellular plants and animals,has been proposed to be potentially associated with some important biological processes such as gene expression regulation and oncogenic pathways(Wion and Casadesus,2006;Boulias and Greer,2022).Yet,recent studies highlighted the arguments on the rarity,source,and origin of 6mA in invertebrates and vertebrates(Boulias and Greer,2022).

关键词： ciliate origin

Crystal Structures of Arabidopsis thaliana Nudix Hydrolase NUDT7 Reveal a Previously Unobserved Conformation

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Molecular Plant 2015年第10期8卷 1557-1559页

作者： Qingyu Tang Caifeng Liu Chen Zhong jianping ding National Center for Protein Sciences Shanghai State Key Laboratory of Molecular Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences 320 Yue-Yang Road Shanghai 200031 China State Key Laboratory of Bioorganic and Natural Products Chemistry Shanghai institute of Organic Chemistry Chinese Academy of Sciences 345 Lingling Road Shanghai 200032 China School of Life Science and Technology Shanghai Tech University 319 Yue-Yang Road Shanghai 200031 China

Dear Editor,Nudix hydrolases are a superfamily of phylogenetically widespread enzymes that catalyze the hydrolysis of nucleoside diphosphate linked to another moiety X （NDP-X） to yield nucleoside monophosphate and P-X. Within the superfamily, at least four families are classified based on their substrate specificities： the Mutt family hydrolases, the ADPR pyrophosphatases, the NADH hydrolases, and the adenosine-（p）n-adenosine hydrolases （Bessman et al., 1996; Gabelii et al., 2001）. Arabidopsis thaliana contains 27 Nudix enzymes whose biological functions are not well understood except for NUDT7 （Ogawa et al., 2005）. NUDT7 belongs to the fibroblast growth factor type Nudix enzyme （FGFTNE） family and shares low sequence identity with other Nudix enzymes with known structures （Gunawardana et al., 2009）. The functional roles of NUDT7 in oxidative stress response and defense response have been demonstrated by genetic studies （Ge et al., 2007; Wang et al., 2013）. It has hydrolase activities toward ADPR and NADH; however, whether ADPR is a physiological substrate of NUDT7 remains obscure （Ge et al., 2007; Wang et al., 2013）.

关键词： hydrolase physiological substrate

Impact of the spatial coherence on self-interference digital holography

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Chinese Physics B 2021年第8期30卷 31-41页

作者： Xingbing Chao Yuan Gao jianping ding Hui-Tian Wang National Laboratory of Solid State Microstructures and School of Physics Nanjing UniversityNanjing 210093China Collaborative Innovation Center of Advanced Microstructures Nanjing UniversityNanjing 210093China Collaborative Innovation Center of Solid-State Lighting and Energy-Saving Electronics Nanjing UniversityNanjing 210093China College of Science Jiujiang UniversityJiujiang 332005China

Owing to the unique feature that the signal and reference waves of self-interference digital holography(SIDH)contain the same spatial information from the same point of object,compared with conventional digital holography,the SIDH has the special spatial coherence *** present a statistical optics approach to analyzing the formation of cross-correlation image in *** study reveals that the spatial coherence of illumination light can greatly influence the imaging characteristics of SIDH,and the impact extent of the spatial coherence depends substantially on the recording distance of *** theoretical conclusions are supported well by numerical simulation and optical experiments.

关键词： holography imaging and optical processing photon statistics and coherence theory interference

Crystal Structure of Cytidine Deaminase Human APOBEC3F Chimeric Catalytic Domain in Complex with DNA

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Chinese Journal of Chemistry 2018年第12期36卷 1241-1248页

作者： Chao Cheng Tianlong Zhang Chunxi Wang Wenxian Lan jianping ding Chunyang Cao State Key Laboratory of Bioorganic and Natural Product Chemistry Center for Excellence in Molecular SynthesisShanghai Institute of Organic ChemistryChinese Academy of Sciences345 Lingling RoadShanghai200032China Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences320 Yueyang RoadShanghai200031China University of Chinese Academy of Sciences No.19(A)Yuquan RoadShijingshan DistrictBeijing 100049China

APOBEC3F (A3F) demonstrates antivirus activity through its A3F‐CD2 domain catalyzing deamination of cytidine in target motif 5’‐TC in viral cDNA during reverse transcription. But structural basis is unclear. Previously, chimeric A3F‐CD2 ( i.e ., A3Fc‐CD2, where residues 195—217 of A3F‐CD2 were replaced with residues 197—221 of A3G‐CD2) was found soluble with deamination activity. Here, we report crystal structures of A3Fc‐CD2 in complexes with single‐stranded DNA (5’‐ATTTT 5 C 6 A 7 A 8 T 9 T‐3’ and 5’‐ATTTT 5 C 6 A 7 A 8 C 9 T‐3’) at resolutions of 1.98 Å and 2.30 Å, respectively. They demonstrate that one molecular DNA binds two A3Fc‐CD2 molecules (monomers A and B) at two sites, distinct from the reported complex structure of human A3F‐CD2 with a 10‐dT DNA. The first site is formed by residues Tyr 333 , Lys 358 and Tyr 359 in monomer A, far away from Zn 2+ binding motif, interacting with bases dT 5 , dC 6 and dA 7 through π‐π stacking and hydrogen bonds. The second site is composed of Trp 277 , Y 307 YFW 310 near to Zn 2+ binding region in monomer B, interacting with base dA 8 , mainly through π‐π stacking and hydrophobic interactions, determining deamination preference of DNA sequence. Subsequent biochemical investigations further confirm the contribution of these residues to DNA binding and deamination activities. These studies are helpful to understand the mechanism how A3F‐CD2 catalyzes cytidine deamination.

关键词： APOBEC3F HIV‐1 deamination DNA structure

Combinatorial analysis on spatial information statistics for the karst water environment in Guiyang,China

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Chinese Journal Of Geochemistry 2012年第2期31卷 195-203页

作者： WANG Zhongmei ZHU Lijun YANG Ruidong YANG Shengyuan ding jianping YANG Genlan College of Resources and Environmental Engineering of Guizhou University Guiyang 550003 China Key Laboratory of Karst Environment and Geohazard Prevention （Guizhou University） Ministry of Education Guiyang 550003 China Guizhou Institute of Geological Environment Monitor Guiyang 550001 China

The karst groundwater system is extremely vulnerable and easily contaminated by human *** understand the spatial distribution of contaminants in the groundwater of karst urban areas and contributors to the contamination,this paper employs the spatial information statistics analysis theory and method to analyze the karst groundwater environment in Guiyang *** on the karst ground water quality data detected in 61 detection points of the research area in the last three years,we made Kriging evaluation isoline map with some ions in the karst groundwater,such as SO4 2-,Fe 3+,Mn 2+and F -,analyzed and evaluated the spatial distribution,extension and variation of four types of ions on the basis of this isoline *** results of the analysis show that the anomaly areas of SO4 2-,Fe 3+,Mn 2+,Fand other ions are mainly located in Baba’ao,Mawangmiao and Sanqiao in northwestern Gui- yang City as well as in its downtown area by reasons of the original non-point source pollution and the contamination caused by human activities(industrial and domestic pollution).

关键词：岩溶地下水空间信息统计地下水环境贵阳市组合分析地下水污染中国人类活动

Molecular basis for the functions of dominantly active Y35N and inactive D60K Rheb mutants in mTORC1 signaling

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Journal of Molecular Cell Biology 2020年第9期12卷 741-744页

作者： Chunxiao Zhang Yan Liu Yifang Zhang Xiangxiang Wang Tianlong Zhang jianping ding State Key Laboratory of Molecular Biology Shanghai Institute of Biochemistry and Cell BiologyCenter for Excellence in Molecular Cell ScienceUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China School of Life Sciences Shanghai UniversityShanghai 200444China School of Life Science Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhou 310024China

Dear Editor,Mammalian target of rapamycin complex 1(mTORC1)serves as a central regulator of cell growth and proliferation by integrating signals from growth factors,nutrients,energy status,and cellular stress(Saxton and Sabatini,2017).A small GTPase,called Ras homolog enriched in brain(Rheb),is a positive regulator of *** other small GTPases,the function of Rheb is dictated by its guanine nucleotide binding states:it is active in the GTP-bound form and inactive in the GDP-bound form(Aspuria and Tamanoi,2004).

关键词： inactive mTORC1 integrating

Dynamic shaping of vectorial optical fields based on two-dimensional blazed holographic grating

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Chinese Physics B 2020年第1期29卷 76-81页

作者： Xinyi Wang Yuan Gao Zhaozhong Chen jianping ding Hui-Tian Wang National Laboratory of Solid State Microstructures and School of Physics Nanjing UniversityNanjing 210093China Collaborative Innovation Center of Advanced Microstructures Nanjing UniversityNanjing 210093China Collaborative Innovation Center of Solid-State Lighting and Energy-Saving Electronics Nanjing UniversityNanjing 210093China

We propose a vectorial optical field generation system based on two-dimensional blazed grating to high-efficiently generate structured optical fields with prescribed amplitude,phase,and *** this system,an optimized blazed grating hologram is written on a spatial light modulator(SLM)and can diffract the majority of the incident light into the first-order diffractions of the x and y directions,which then serve as base vectors for synthesizing desired vector *** with the conventional cosine grating used in the previous work,the proposed two-dimensional,blazed grating has a much higher *** computer simulation and optical experiment validate that a conversion efficiency up to 5 times that of the former work is *** method can facilitate applications of the optical field manipulation.

关键词： diffraction polarization holographic gratings liquid-crystal devices

Three-dimensional multiple optical cages formed by focusing double-ring shaped radially and azimuthally polarized beams

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Chinese Optics Letters 2018年第3期16卷 44-47页

作者： Tingting Zeng jianping ding National Laboratory of Solid Microstructure and School of Physics Nanjing University Nanjing 210093 China

We propose and simulate a method for generating a three-dimensional （3D） optical cage in the vicinity of focus by focusing a double-ring shaped radially and azimuthally polarized beam. Our study shows that the combination of an inner ring with an azimuthally polarized field and an outer ring with a radially polarized field and a phase factor can produce an optical cage with a dark region enclosed by higher intensity. The shape of the cage can be tailored by appropriately adjusting the parameters of double-mode beams. Furthermore, multiple 3D optical cages can be realized by applying the shift theorem of the Fourier transform and macro-pixel sampling algorithm to a double-ring shaped radially and azimuthally polarized beam.

关键词： Three-dimensional multiple optical cages formed by focusing double-ring shaped radially and azimuthally polarized beams