1
|
Jia Q, Zeng H, Li M, Tang J, Xiao N, Gao S, Li H, Zhang J, Zhang Z, Xie W. Binding asymmetry and conformational studies of the AtGSDA dimer. Comput Struct Biotechnol J 2023; 21:5515-5522. [PMID: 38022696 PMCID: PMC10663702 DOI: 10.1016/j.csbj.2023.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023] Open
Abstract
Guanosine deaminase (GSDA) is an important deaminase that converts guanosine to xanthosine, a key intermediate in nitrogen recycling in plants. We previously solved complex structures of Arabidopsis thaliana GSDA bound by various ligands and examined its catalytic mechanism. Here, we report cocrystal structures of AtGSDA bound by inactive guanosine derivatives, which bind relatively weakly to the enzyme and mostly have poor binding geometries. The two protomers display unequal binding performances, and molecular dynamics simulation identified diverse conformations during the enzyme-ligand interactions. Moreover, intersubunit, tripartite salt bridges show conformational differences between the two protomers, possibly acting as "gating" systems for substrate binding and product release. Our structural and biochemical studies provide a comprehensive understanding of the enzymatic behavior of this intriguing enzyme.
Collapse
Affiliation(s)
- Qian Jia
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Hui Zeng
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Mingwei Li
- Division of Life Sciences and Medicine, and Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Jing Tang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Nan Xiao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Shangfang Gao
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Huanxi Li
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Jinbing Zhang
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| | - Zhiyong Zhang
- MOE Key Laboratory for Membraneless Organelles & Cellular Dynamics, Department of Physics, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Wei Xie
- MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China
| |
Collapse
|
2
|
Rallapalli KL, Ranzau BL, Ganapathy KR, Paesani F, Komor AC. Combined Theoretical, Bioinformatic, and Biochemical Analyses of RNA Editing by Adenine Base Editors. CRISPR J 2022; 5:294-310. [PMID: 35353638 DOI: 10.1089/crispr.2021.0131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Adenine base editors (ABEs) have been subjected to multiple rounds of mutagenesis with the goal of optimizing their function as efficient and precise genome editing agents. Despite an ever-expanding data set of ABE mutants and their corresponding DNA or RNA-editing activity, the molecular mechanisms defining these changes remain to be elucidated. In this study, we provide a systematic interpretation of the nature of these mutations using an entropy-based classification model that relies on evolutionary data from extant protein sequences. Using this model in conjunction with experimental analyses, we identify two previously reported mutations that form an epistatic pair in the RNA-editing functional landscape of ABEs. Molecular dynamics simulations reveal the atomistic details of how these two mutations affect substrate-binding and catalytic activity, via both individual and cooperative effects, hence providing insights into the mechanisms through which these two mutations are epistatically coupled.
Collapse
Affiliation(s)
- Kartik L Rallapalli
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Brodie L Ranzau
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Kaushik R Ganapathy
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA.,Materials Science and Engineering, University of California San Diego, La Jolla, California, USA; and University of California San Diego, La Jolla, California, USA.,San Diego Supercomputer Center, University of California San Diego, La Jolla, California, USA
| | - Alexis C Komor
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, USA; University of California San Diego, La Jolla, California, USA
| |
Collapse
|
3
|
Zhao G, Peng W, Song K, Shi J, Lu X, Wang B, Du YL. Molecular basis of enzymatic nitrogen-nitrogen formation by a family of zinc-binding cupin enzymes. Nat Commun 2021; 12:7205. [PMID: 34893622 PMCID: PMC8664883 DOI: 10.1038/s41467-021-27523-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 11/19/2021] [Indexed: 11/26/2022] Open
Abstract
Molecules with a nitrogen-nitrogen (N-N) bond in their structures exhibit various biological activities and other unique properties. A few microbial proteins are recently emerging as dedicated N-N bond forming enzymes in natural product biosynthesis. However, the details of these biochemical processes remain largely unknown. Here, through in vitro biochemical characterization and computational studies, we report the molecular basis of hydrazine bond formation by a family of di-domain enzymes. These enzymes are widespread in bacteria and sometimes naturally exist as two standalone enzymes. We reveal that the methionyl-tRNA synthase-like domain/protein catalyzes ATP-dependent condensation of two amino acids substrates to form a highly unstable ester intermediate, which is subsequently captured by the zinc-binding cupin domain/protein and undergoes redox-neutral intramolecular rearrangement to give the N-N bond containing product. These results provide important mechanistic insights into enzymatic N-N bond formation and should facilitate future development of novel N-N forming biocatalyst.
Collapse
Affiliation(s)
- Guiyun Zhao
- grid.13402.340000 0004 1759 700XState Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003 Hangzhou, China ,grid.13402.340000 0004 1759 700XInstitute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 310058 Hangzhou, China
| | - Wei Peng
- grid.12955.3a0000 0001 2264 7233State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005 Xiamen, China
| | - Kaihui Song
- grid.13402.340000 0004 1759 700XInstitute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 310058 Hangzhou, China
| | - Jingkun Shi
- grid.13402.340000 0004 1759 700XInstitute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 310058 Hangzhou, China
| | - Xingyu Lu
- grid.494629.40000 0004 8008 9315Key Laboratory of Precise Synthesis of Functional Molecules of Zhejiang Province, School of Science, Instrumentation and Service Center for Molecular Sciences, Westlake University, 310024 Hangzhou, China
| | - Binju Wang
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, 361005, Xiamen, China.
| | - Yi-Ling Du
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, China. .,Institute of Pharmaceutical Biotechnology, School of Medicine, Zhejiang University, 310058, Hangzhou, China.
| |
Collapse
|