Ribocentre: a database of ribozymes

Author:

Deng Jie1,Shi Yaohuang23,Peng Xuemei1,He Yuanlin1,Chen Xiaoxue14,Li Mengxiao1,Lin Xiaowei15,Liao Wenjian15ORCID,Huang Yuanyin1,Jiang Taijiao3,Lilley David M J6,Miao Zhichao37ORCID,Huang Lin1ORCID

Affiliation:

1. Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou 510120 , China

2. School of Life Science and Technology, ShanghaiTech University , Shanghai , 201210 , China

3. Guangzhou Laboratory, Guangzhou International Bio Island , Guangzhou 510005 , China

4. Department of pharmacy, Sun-Yat-Sen Memorial Hospital, Sun Yat-sen University , Guangzhou 510120 , China

5. Department of Urology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University , Guangzhou 510120 , China

6. Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee , Dow Street, Dundee DD1 5EH, UK

7. Translational Research Institute of Brain and Brain-Like Intelligence and Department of Anesthesiology, Shanghai Fourth People's Hospital Affiliated to Tongji University School of Medicine , Shanghai 200434 , China

Abstract

Abstract Ribozymes are excellent systems in which to study ‘sequence - structure - function’ relationships in RNA molecules. Understanding these relationships may greatly help structural modeling and design of functional RNA structures and some functional structural modules could be repurposed in molecular design. At present, there is no comprehensive database summarising all the natural ribozyme families. We have therefore created Ribocentre, a database that collects together sequence, structure and mechanistic data on 21 ribozyme families. This includes available information on timelines, sequence families, secondary and tertiary structures, catalytic mechanisms, applications of the ribozymes together with key publications. The database is publicly available at https://www.ribocentre.org.

Funder

Guangdong Science and Technology Department

National Natural Science Foundation of China

Cancer Research UK

National Key Research and Development Program of China

Guangzhou Laboratory

Publisher

Oxford University Press (OUP)

Subject

Genetics

Reference51 articles.

1. Chemistry and biology of self-cleaving ribozymes;Jimenez;Trends Biochem. Sci.,2015

2. Mechanisms of RNA catalysis;Lilley;Philos. Trans. R. Soc. Lond. B Biol. Sci.,2011

3. The structural basis of ribosome activity in peptide bond synthesis;Nissen;Science,2000

4. The ribosome as a versatile catalyst: reactions at the peptidyl transferase center;Rodnina;Curr. Opin. Struct. Biol.,2013

5. The mechanism of peptidyl transfer catalysis by the ribosome;Leung;Annu. Rev. Biochem.,2011

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