Discovery of deaminase functions by structure-based protein clustering

Huang, Jinyan; Lin, Qiupeng; Fei, Hongyuan; He, Zhi‐Guo; Xu, Hu; Li, Yunjia; Qu, Kunli; Han, Peng; Gao, Qiang; Li, Boshu; Liu, Guanwen; Zhang, Lixiao; Hu, Jiajia; Zhang, Rui; Zuo, Erwei; Luo, Yonglun; Ran, Yidong; Qiu, Jian; Zhao, Kevin T.; Gao, Caixia

doi:10.1016/j.cell.2023.05.041

Cited by 60 publications

(33 citation statements)

References 60 publications

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“…identified some novel deaminases with disparate deamination motif preferences on ssDNA substrates, including Sdd3, Sdd6, and Sdd7, which would further expand the editing scope of base editors ( Table 1 ). Though these Sdds share a core structure similar to DddA and theoretically do not belong to the APOBEC/AID family, they showed more robust cytosine base editing activity on ssDNA than some APOBEC/AID deaminases and could be used to develop base editing tools (Huang et al 2023 ).…”

Section: Cytidine Deaminasementioning

confidence: 99%

“…Notably, DddA targets double-stranded DNA (dsDNA) instead of single-stranded DNA (ssDNA) (Mok et al 2020 ; Salter and Smith 2018 ), enabling it to fulfill editing goals at places where other deaminases cannot reach (Kim and Chen 2023 ). More recently, AI-based protein structure prediction and clustering established a suite of ssDNA deaminases and dsDNA deaminases, further enriching the deaminases tool family (Huang et al 2023 ).…”

Section: Introductionmentioning

confidence: 99%

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Nucleoside deaminases: the key players in base editing toolkit

Xiang,

Xu,

et al. 2023

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The development of nucleoside deaminase-containing base editors realized targeted single base change with high efficiency and precision. Such nucleoside deaminases include adenosine and cytidine deaminases, which can catalyze adenosine-to-inosine (A-to-I) and cytidine-to-uridine (C-to-U) conversion respectively. These nucleoside deaminases are under the spotlight because of their vast application potential in gene editing. Recent advances in the engineering of current nucleoside deaminases and the discovery of new nucleoside deaminases greatly broaden the application scope and improve the editing specificity of base editors. In this review, we cover current knowledge about the deaminases used in base editors, including their key structural features, working mechanisms, optimization, and evolution.

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Section: Cytidine Deaminasementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Nucleoside deaminases: the key players in base editing toolkit

Xiang,

Xu,

et al. 2023

swwlxb

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“…Consequently, it fails to fully capture the functional attributes of proteins, including core amino acids, overall sequence identity, and specific motifs . Solving the three-dimensional (3D) structure of proteins is critical for unraveling their functional properties, offering a reliable and rational perspective on protein function during the processes of mining, clustering, and classification. − Benefiting from rapidly developing artificial intelligence (AI) methods, it is possible to combine amino acid sequences with high-resolution 3D protein structures to mine and classify proteins with specific functions on a large scale.…”

Section: Introductionmentioning

confidence: 99%

Sequence- and Structure-Based Mining of Thermostable D-Allulose 3-Epimerase and Computer-Guided Protein Engineering To Improve Enzyme Activity

Qi,

Wang,

et al. 2023

J. Agric. Food Chem.

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D-Allulose, a functional sweetener, can be synthesized from fructose using D-allulose 3-epimerase (DAEase). Nevertheless, a majority of the reported DAEases have inadequate stability under harsh industrial reaction conditions, which greatly limits their practical applications. In this study, big data mining combined with a computer-guided free energy calculation strategy was employed to discover a novel DAEase with excellent thermostability. Consensus sequence analysis of flexible regions and comparison of binding energies after substrate docking were performed using phylogeny-guided big data analyses. TtDAE from Thermogutta terrifontis was the most thermostable among 358 candidate enzymes, with a half-life of 32 h at 70 °C. Subsequently, structure-guided virtual screening and a customized strategy based on a combinatorial active-site saturation test/iterative saturation mutagenesis were utilized to engineer TtDAE. Finally, the catalytic activity of the M4 variant (P105A/L14C/T63G/I65A) was increased by 5.12-fold. Steered molecular dynamics simulations indicated that M4 had an enlarged substrate-binding pocket, which enhanced the fit between the enzyme and the substrate. The approach presented here, combining DAEases mining with further rational modification, provides guidance for obtaining promising catalysts for industrial-scale production.

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“…Subsequently, the distance matrix of the structures within the protein set is calculated, and a phylogenetic tree is constructed. An exciting analogous case of this workflow is that Huang et al discovered novel base editing tools by structure clustering within a protein family . In particular, this structural analysis workflow is nearly identical to the sequence-based workflow, with the primary distinction being the shift in the analytical subject from sequence to structure.…”

mentioning

confidence: 99%

“…An exciting analogous case of this workflow is that Huang et al discovered novel base editing tools by structure clustering within a protein family. 3 In particular, this structural analysis workflow is nearly identical to the sequence-based workflow, with the primary distinction being the shift in the analytical subject from sequence to structure. In other words, sequence-based analysis theories can be transplanted to structure-based analysis.…”

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confidence: 99%

Entering an Era of Protein Structuromics

Wu,

Liu,

et al. 2023

Biochemistry

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Sequence determines the structure, and the structure in turn determines the function, are the fundamental principles of protein chemistry. In the genomics era, the paradigm of mining protein functionality and evolutionary insights through sequence analysis has led to remarkable achievements. However, protein sequences often mutate faster than their structural counterparts during evolution. For protein sets characterized by highly divergent sequences, sequence-based analysis is often inadequate, whereas direct extraction of implicit information from the structures appears to be a more effective strategy.

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Discovery of deaminase functions by structure-based protein clustering

Cited by 60 publications

References 60 publications

Nucleoside deaminases: the key players in base editing toolkit

Nucleoside deaminases: the key players in base editing toolkit

Sequence- and Structure-Based Mining of Thermostable D-Allulose 3-Epimerase and Computer-Guided Protein Engineering To Improve Enzyme Activity

Entering an Era of Protein Structuromics

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