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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.
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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
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2
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Wei Y, Shen H, Gao C, Du Y, Zhao Y, Wang Y, Zhou S, Li J, Zhao B, Wu D. Electrochemical detection mechanism of estrogen effect induced by cadmium: The regulation of purine metabolism by the estrogen effect of cadmium. CHEMOSPHERE 2023; 311:136970. [PMID: 36283430 DOI: 10.1016/j.chemosphere.2022.136970] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 09/20/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Some heavy metals in the environment may have estrogen-like activity, which probably lead to major diseases such as breast cancer. It is of great importance to establish new methods to evaluate the estrogen effect of heavy metals from multiple angles due to the complex mechanism of estrogen effect. In this paper, using MCF-7 cells as model, the electrochemical detection mechanism of the estrogen effect of heavy metal cadmium (Cd) was studied. The two electrochemical signals of MCF-7 cells derived from uric acid (0.30 V) and the mixture of guanine and xanthine (0.68 V) increased in a time and dose-dependent manner when MCF-7 cells induced by Cd, reaching the maximum at 96 h and 10-9 mol L-1. Further studies found that three purine metabolism pathways about de novo synthesis, salvage synthesis and decomposition metabolism were activated by the estrogen effect of Cd. The expression of PRPP amidotransferase in purine de novo synthesis pathway and HPRT in purine salvage synthesis pathway up-regulated, especially HPRT, which promoted cell proliferation together. Nevertheless, the expression of GDA and ADA, the key enzymes in purine decomposition metabolism pathway, up-regulated in a time and dose-dependent manner, which had same tendency with that of ERα, thereby increased the content of intracellular hypoxanthine, guanine, xanthine and uric acid, and enhanced electrochemical signals.
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Affiliation(s)
- Ying Wei
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, 154007, PR China
| | - Hongkuan Shen
- Jiamusi Inspection and Testing Center, Jiamusi, Heilongjiang, 154007, PR China
| | - Changsheng Gao
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, 154007, PR China
| | - Yuan Du
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi, Heilongjiang, 154007, PR China
| | - Yanli Zhao
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi, Heilongjiang, 154007, PR China
| | - Yuhang Wang
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, 154007, PR China
| | - Shi Zhou
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, 154007, PR China
| | - Jinlian Li
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi, Heilongjiang, 154007, PR China.
| | - Baojiang Zhao
- Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi, Heilongjiang, 154007, PR China.
| | - Dongmei Wu
- College of Pharmacy, Jiamusi University, Jiamusi, Heilongjiang, 154007, PR China; Heilongjiang Provincial Key Laboratory of New Drug Development and Pharmacotoxicological Evaluation, Jiamusi, Heilongjiang, 154007, PR China.
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3
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Wei Y, Gao C, Cui J, Shen H, Zhao Y, Zhou S, Ye C, Du Y, Li J, Wu D. The response of electrochemical method to estrogen effect and the tolerance to culture factors: Comparison with MTT and cell counting methods. Anal Chim Acta 2022; 1233:340514. [DOI: 10.1016/j.aca.2022.340514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/20/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022]
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4
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Jia Q, Zeng H, Li H, Xiao N, Tang J, Gao S, Zhang J, Xie W. The C-terminal loop of Arabidopsis thaliana guanosine deaminase is essential to catalysis. Chem Commun (Camb) 2021; 57:9748-9751. [PMID: 34477187 DOI: 10.1039/d1cc03042f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Guanosine deaminase (GSDA) in plants specifically deaminates (de)guanosine to produce xanthosine with high specificity, which is further converted to xanthine, a key intermediate in purine metabolism and nitrogen recycling. We solved GSDA's structures from Arabidopsis thaliana in the free and ligand-bound forms at high resolutions. Unlike GDA, the enzyme employs a single-proton shuttle mechanism for catalysis and both the substrate and enzyme undergo structural rearrangements. The last fragment of the enzyme loops back and seals the active site, and the substrate rotates during the reaction, both essential to deamination. We further identified more substrates that could be employed by the enzyme and compare it with other deaminases to reveal the recognition differences of specific substrates. Our studies provide insight into this important enzyme involved in purine metabolism and will potentially aid in the development of deaminase-based gene-editing tools.
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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.
| | - 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.
| | - 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.
| | - 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.
| | - 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.
| | - 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.
| | - 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.
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5
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Sen A, Gaded V, Jayapal P, Rajaraman G, Anand R. Insights into the Dual Shuttle Catalytic Mechanism of Guanine Deaminase. J Phys Chem B 2021; 125:8814-8826. [PMID: 34324362 DOI: 10.1021/acs.jpcb.1c06127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanine deaminases (GD) are essential enzymes that help in regulating the nucleobase pool. Since the deamination reaction can result in the accumulation of mutagenic bases that can lead to genomic instability, these enzymes are tightly regulated and are nonpromiscuous. Here, we delineate the basis of their substrate fidelity via entailing the reaction mechanism of deamination by employing density functional theory (DFT) calculations on NE0047, a GD from Nitrosomonas europaea. The results show that, unlike pyrimidine deaminases, which require a single glutamic acid as a proton shuttle, GDs involve two amino acids, E79 and E143 (numbering in NE0047), which control its reactivity. The hybrid quantum mechanics/molecular mechanics (QM/MM) calculations have shown that the first Zn-bound proton transfer to the N3 atom of the substrate is mediated by the E79 residue, and the second proton is transferred to the amine nitrogen of substrate via E143. Moreover, cluster models reveal that the crystallographic water molecules near the active site control the reactivity. A comparison with human GD reveals that the proposed catalytic mechanism is generic, and the knowledge generated here can be effectively applied to design selective inhibitors.
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Affiliation(s)
- Asmita Sen
- Department of Chemistry, Indian Institute of Technology-Bombay, Mumbai 400076, India
| | - Vandana Gaded
- Department of Chemistry, Indian Institute of Technology-Bombay, Mumbai 400076, India
| | - Prabha Jayapal
- Department of Chemistry, Indian Institute of Technology-Bombay, Mumbai 400076, India
| | - Gopalan Rajaraman
- Department of Chemistry, Indian Institute of Technology-Bombay, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology-Bombay, Mumbai 400076, India
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6
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Chen SC, Ye LC, Yen TM, Zhu RX, Li CY, Chang SC, Liaw SH, Hsu CH. Crystal structures of Aspergillus oryzae Rib2 deaminase: the functional mechanism involved in riboflavin biosynthesis. IUCRJ 2021; 8:549-558. [PMID: 34258004 PMCID: PMC8256712 DOI: 10.1107/s205225252100275x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/15/2021] [Indexed: 06/13/2023]
Abstract
Riboflavin serves as the direct precursor of the FAD/FMN coenzymes and is biosynthesized in most prokaryotes, fungi and plants. Fungal Rib2 possesses a deaminase domain for deamination of pyrimidine in the third step of riboflavin biosynthesis. Here, four high-resolution crystal structures of a Rib2 deaminase from Aspergillus oryzae (AoRib2) are reported which display three distinct occluded, open and complex forms that are involved in substrate binding and catalysis. In addition to the deaminase domain, AoRib2 contains a unique C-terminal segment which is rich in charged residues. Deletion of this unique segment has no effect on either enzyme activity or protein stability. Nevertheless, the C-terminal αF helix preceding the segment plays a role in maintaining protein stability and activity. Unexpectedly, AoRib2 is the first mononucleotide deaminase found to exist as a monomer, perhaps due to the assistance of its unique longer loops (Lβ1-β2, LαB-β3 and LαC-β4). These results form the basis for a molecular understanding of riboflavin biosynthesis in fungi and might assist in the development of antibiotics.
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Affiliation(s)
- Sheng-Chia Chen
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Li-Ci Ye
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
| | - Te-Ming Yen
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei 11217, Taiwan
| | - Ruei-Xin Zhu
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
| | - Cheng-Yu Li
- Department of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - San-Chi Chang
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Shwu-Huey Liaw
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei 11221, Taiwan
- Department of Medical Research and Education, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Chun-Hua Hsu
- Department of Agricultural Chemistry, National Taiwan University, Taipei 10617, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei 10617, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei 10617, Taiwan
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7
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Singh J, Gaded V, Bitra A, Anand R. Structure guided mutagenesis reveals the substrate determinants of guanine deaminase. J Struct Biol 2021; 213:107747. [PMID: 34010666 DOI: 10.1016/j.jsb.2021.107747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/05/2021] [Accepted: 05/13/2021] [Indexed: 10/21/2022]
Abstract
Guanine deaminases (GDs) are essential enzymes that regulate the overall nucleobase pool. Since the deamination of guanine to xanthine results in the production of a mutagenic base, these enzymes have evolved to be very specific in nature. Surprisingly, they accept structurally distinct triazine ammeline, an intermediate in the melamine pathway, as one of the moonlighting substrates. Here, by employing NE0047 (a GD from Nitrosomonas europaea), we delineate the nuance in the catalytic mechanism that allows these two distinct substrates to be catalyzed. A combination of enzyme kinetics, X-ray crystallographic, and calorimetric studies reveal that GDs operate via a dual proton shuttle mechanism with two glutamates, E79 and E143, crucial for deamination. Additionally, N66 appears to be central for substrate anchoring and participates in catalysis. The study highlights the importance of closure of the catalytic loop and of maintenance of the hydrophobic core by capping residues like F141 and F48 for the creation of an apt environment for activation of the zinc-assisted catalysis. This study also analyzes evolutionarily distinct GDs and asserts that GDs incorporate subtle variations in the active site architectures while keeping the most critical active site determinants conserved.
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Affiliation(s)
- Jayanti Singh
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Vandana Gaded
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Aruna Bitra
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai, Maharashtra 400076, India.
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8
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Trancoso I, Morimoto R, Boehm T. Co-evolution of mutagenic genome editors and vertebrate adaptive immunity. Curr Opin Immunol 2020; 65:32-41. [PMID: 32353821 PMCID: PMC7768089 DOI: 10.1016/j.coi.2020.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 02/18/2020] [Accepted: 03/02/2020] [Indexed: 12/28/2022]
Abstract
The adaptive immune systems of all vertebrates rely on self-DNA mutating enzymes to assemble their antigen receptors in lymphocytes of their two principal lineages. In jawed vertebrates, the RAG1/2 recombinase directs V(D)J recombination of B cell and T cell receptor genes, whereas the activation-induced cytidine deaminase AID engages in their secondary modification. The recombination activating genes (RAG) 1 and 2 evolved from an ancient transposon-encoded genome modifier into a self-DNA mutator serving adaptive immunity; this was possible as a result of domestication, involving several changes in RAG1 and RAG2 proteins suppressing transposition and instead facilitating-coupled cleavage and recombination. By contrast, recent evidence supports the notion that the antigen receptors of T-like and B-like cells of jawless vertebrates, designated variable lymphocyte receptors (VLRs), are somatically assembled through a process akin to gene conversion that is believed to be dependent on the activities of distant relatives of AID, the cytidine deaminases CDA1 and CDA2, respectively. It appears, therefore, that the precursors of AID and CDAs underwent a domestication process that changed their target range from foreign nucleic acids to self-DNA; this multi-step evolutionary process ensured that the threat to host genome integrity was minimized. Here, we review recent findings illuminating the evolutionary steps associated with the domestication of the two groups of genome editors, RAG1/2 and cytidine deaminases, indicating how they became the driving forces underlying the emergence of vertebrate adaptive immune systems.
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Affiliation(s)
- Inês Trancoso
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Ryo Morimoto
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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9
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Daley SK, Cordell GA. Homopurine Alkaloids: A Brief Overview. Nat Prod Commun 2020. [DOI: 10.1177/1934578x20917787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The isolation, structure elucidation, synthesis, biological properties, and biosynthesis of the homopurine alkaloids are reviewed, with an emphasis on the “victim-guardian” relationships between co-occurring alkaloids.
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Affiliation(s)
| | - Geoffrey A. Cordell
- Natural Products Inc., Evanston, IL, USA
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL, USA
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10
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Shek R, Hilaire T, Sim J, French JB. Structural Determinants for Substrate Selectivity in Guanine Deaminase Enzymes of the Amidohydrolase Superfamily. Biochemistry 2019; 58:3280-3292. [PMID: 31283204 DOI: 10.1021/acs.biochem.9b00341] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Guanine deaminase is a metabolic enzyme, found in all forms of life, which catalyzes the conversion of guanine to xanthine. Despite the availability of several crystal structures, the molecular determinants of substrate orientation and mechanism remain to be elucidated for the amidohydrolase family of guanine deaminase enzymes. Here, we report the crystal structures of Escherichia coli and Saccharomyces cerevisiae guanine deaminase enzymes (EcGuaD and Gud1, respectively), both members of the amidohydrolase superfamily. EcGuaD and Gud1 retain the overall TIM barrel tertiary structure conserved among amidohydrolase enzymes. Both proteins also possess a single zinc cation with trigonal bipyrimidal coordination geometry within their active sites. We also determined a liganded structure of Gud1 bound to the product, xanthine. Analysis of this structure, along with kinetic data of native and site-directed mutants of EcGuaD, identifies several key residues that are responsible for substrate recognition and catalysis. In addition, after a small library of compounds had been screened, two guanine derivatives, 8-azaguanine and 1-methylguanine, were identified as EcGuaD substrates. Interestingly, both EcGuaD and Gud1 also exhibit secondary ammeline deaminase activity. Overall, this work details key structural features of substrate recognition and catalysis of the amidohydrolase family of guanine deaminase enzymes in support of our long-term goal to engineer these enzymes with altered activity and substrate specificity.
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Affiliation(s)
- Roger Shek
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Tylene Hilaire
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jasper Sim
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States
| | - Jarrod B French
- Department of Biochemistry and Cell Biology , Stony Brook University , Stony Brook , New York 11794 , United States.,Department of Chemistry , Stony Brook University , Stony Brook , New York 11794 , United States
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Terashima M, Ohashi K, Takasuka TE, Kojima H, Fukui M. Antarctic heterotrophic bacterium Hymenobacter nivis P3 T displays light-enhanced growth and expresses putative photoactive proteins. ENVIRONMENTAL MICROBIOLOGY REPORTS 2019; 11:227-235. [PMID: 30298689 DOI: 10.1111/1758-2229.12702] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 10/02/2018] [Indexed: 06/08/2023]
Abstract
Hymenobacter nivis P3T is a heterotrophic bacterium isolated from Antarctic red snow generated by algal blooms. Despite being non-photosynthetic, H. nivis was dominantly found in the red snow environment that is exposed to high light and UV irradiation, suggesting that this species can flourish under such harsh conditions. In order to further understand the adaptive strategies on the snow surface environment of Antarctica, the genome of H. nivis P3T was sequenced and analyzed, which identified genes putatively encoding for light-reactive proteins such as proteorhodopsin, phytochrome, photolyase and several copies of cryptochromes. Culture-based experiments revealed that H. nivis P3T growth was significantly enhanced under light conditions, while dark conditions had increased extracellular polymeric substances. Furthermore, the expression of several putative light-reactive proteins was determined by proteomic analysis. These results indicate that H. nivis P3T is able to potentially utilize light, which may explain its dominance on the red snow surface environment of Antarctica. ORIGINALITY-SIGNIFICANCE STATEMENT: The role of proteorhodopsin in heterotrophic bacteria is not well-characterized, as only a handful of proteorhodopsin-harbouring isolates were shown to have a light-enhanced phenotype through culture-based experiments to date. This is the first study that demonstrates light-stimulated growth and protein expression evidence of photoactive proteins for a non-marine psychrophile and for a member of the genus Hymenobacter. It is also the first study that provides comprehensive proteome information for this genus. This study presents significant results in understanding the adaptive mechanism of a heterotrophic non-photosynthetic bacterium thriving on the snow surface environment of Antarctica as well as demonstrating the role of light-utilization in promoting growth, possibly through proteorhodopsin.
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Affiliation(s)
- Mia Terashima
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, 060-0819, Japan
| | - Keisuke Ohashi
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Kita-ku, Sapporo, 060-8589, Japan
| | - Hisaya Kojima
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, 060-0819, Japan
| | - Manabu Fukui
- Institute of Low Temperature Science, Hokkaido University, Kita-ku, Sapporo, 060-0819, Japan
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12
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iTRAQ-based quantitative proteomics analysis of cold stress-induced mechanisms in grafted watermelon seedlings. J Proteomics 2019; 192:311-320. [DOI: 10.1016/j.jprot.2018.09.012] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 09/05/2018] [Accepted: 09/20/2018] [Indexed: 12/21/2022]
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13
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Pan SA, Sun Y, Li M, Deng WW, Zhang ZZ. Guanine deaminase provides evidence of the increased caffeine content during the piling process of pu'erh tea. RSC Adv 2019; 9:36136-36143. [PMID: 35540571 PMCID: PMC9075041 DOI: 10.1039/c9ra05655f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/31/2019] [Indexed: 12/17/2022] Open
Abstract
Wet piling is a key process for producing pu'erh tea because various components change under the action of microorganisms. Among these components, caffeine content is increased. Evidence has indicated a salvage pathway for caffeine biosynthesis in microbes, in which xanthine is methylated in the order of N-3 → N-1 → N-7. In addition, guanine can be used to synthesize xanthine through guanine deaminase (EC: 3.5.4.3). In this study, we investigated the variation in caffeine content during piling fermentation with supplementary guanine, 15N-labeled guanine and xanthine. We cloned the guanine deaminase gene (GUD1) from Saccharomyces cerevisiae (one dominant strain in piling fermentation). The results revealed that [15N]xanthine could be synthesized from [15N]guanine, and [15N]caffeine was also detected during piling with supplementary [15N]xanthine. Furthermore, ScGUD1 could catalyze the conversion of guanine to xanthine, which is likely to be methylated for caffeine synthesis under microorganism action. The obtained results revealed the mechanism underlying the increased caffeine content during piling of pu'erh tea. Wet piling is a key process for producing pu'erh tea because various components change under the action of microorganisms.![]()
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Affiliation(s)
- Si-an Pan
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
| | - Ying Sun
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
| | - Mengmeng Li
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
| | - Wei-Wei Deng
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
| | - Zheng-Zhu Zhang
- State Key Laboratory of Tea Plant Biology and Utilization
- Anhui Agricultural University
- Hefei
- China
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14
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Mahor D, Prasad GS. Biochemical Characterization of Kluyveromyces lactis Adenine Deaminase and Guanine Deaminase and Their Potential Application in Lowering Purine Content in Beer. Front Bioeng Biotechnol 2018; 6:180. [PMID: 30555824 PMCID: PMC6281700 DOI: 10.3389/fbioe.2018.00180] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 11/12/2018] [Indexed: 11/13/2022] Open
Abstract
Excess amounts of uric acid in humans leads to hyperuricemia, which is a biochemical precursor of gout and is also associated with various other disorders. Gout is termed as crystallization of uric acid, predominantly within joints. The burden of hyperuricemia and gout has increased worldwide due to lifestyle changes, obesity, and consumption of purine-rich foods, fructose-containing drinks, and alcoholic beverages. Some of the therapies available to cure gout are associated with unwanted side-effects and antigenicity. We propose an attractive and safe strategy to reduce purine content in beverages using enzymatic application of purine degrading enzymes such as adenine deaminase (ADA) and guanine deaminase (GDA) that convert adenine and guanine into hypoxanthine and xanthine, respectively. We cloned, expressed, purified, and biochemically characterized both adenine deaminase (ADA) and guanine deaminase (GDA) enzymes that play important roles in the purine degradation pathway of Kluyveromyces lactis, and demonstrate their application in lowering purine content in a beverage. The popular beverage beer has been selected as an experimental sample as it confers higher risks of hyperuricemia and gout. Quantification of purine content in 16 different beers from the Indian market showed varying concentrations of different purines. Enzymatic treatment of beer samples with ADA and GDA showed a reduction of adenine and guanine content, respectively. These enzymes in combination with other purine degrading enzymes showed marked reduction in purine content in beer samples. Both enzymes can work at 5.0–8.0 pH range and retain >50% activity at 40°C, making them good candidates for industrial applications.
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Affiliation(s)
- Durga Mahor
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Gandham S Prasad
- Microbial Type Culture Collection and Gene Bank, CSIR-Institute of Microbial Technology, Chandigarh, India
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Diversification of AID/APOBEC-like deaminases in metazoa: multiplicity of clades and widespread roles in immunity. Proc Natl Acad Sci U S A 2018; 115:E3201-E3210. [PMID: 29555751 PMCID: PMC5889660 DOI: 10.1073/pnas.1720897115] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae. Most vertebrate AADs, including AID and APOBECs1-3, diversified in the vertebrates, whereas the APOBEC4-like clade has a deeper origin in metazoa. Positional entropy analysis suggests that several AAD clades are diversifying rapidly, especially in the positions predicted to interact with the nucleic acid target motif, and with potential viral inhibitors. Further, several AADs have evolved neomorphic metal-binding inserts, especially within loops predicted to interact with the target nucleic acid. We also observe polymorphisms, driven by alternative splicing, gene loss, and possibly intergenic recombination between paralogs. We propose that biological conflicts of AADs with viruses and genomic retroelements are drivers of rapid AAD evolution, suggesting a widespread presence of mutagenesis-based immune-defense systems. Deaminases like AID represent versions "institutionalized" from the broader array of AADs pitted in such arms races for mutagenesis of self-DNA, and similar recruitment might have independently occurred elsewhere in metazoa.
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16
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Gaded V, Anand R. Nucleobase deaminases: a potential enzyme system for new therapies. RSC Adv 2018; 8:23567-23577. [PMID: 35540270 PMCID: PMC9081823 DOI: 10.1039/c8ra04112a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 06/11/2018] [Indexed: 11/21/2022] Open
Abstract
This review presents an overview of the structure, function and mechanism of CDA deaminases and their potential as enzyme systems for development of new antimicrobial therapies.
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Affiliation(s)
- Vandana Gaded
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai
- India
| | - Ruchi Anand
- Department of Chemistry
- Indian Institute of Technology Bombay
- Mumbai
- India
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17
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Gaded V, Anand R. Selective Deamination of Mutagens by a Mycobacterial Enzyme. J Am Chem Soc 2017; 139:10762-10768. [DOI: 10.1021/jacs.7b04967] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Vandana Gaded
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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18
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Abstract
Genomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being 'predicted', while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.
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Affiliation(s)
- Antoine Danchin
- Institute of Cardiometabolism and NutritionHôpital de la Pitié‐Salpêtrière47 Boulevard de l'HôpitalParis75013France
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19
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Wierzchowski J, Antosiewicz JM, Shugar D. 8-Azapurines as isosteric purine fluorescent probes for nucleic acid and enzymatic research. MOLECULAR BIOSYSTEMS 2015; 10:2756-74. [PMID: 25124808 DOI: 10.1039/c4mb00233d] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The 8-azapurines, and their 7-deaza and 9-deaza congeners, represent a unique class of isosteric (isomorphic) analogues of the natural purines, frequently capable of substituting for the latter in many biochemical processes. Particularly interesting is their propensity to exhibit pH-dependent room-temperature fluorescence in aqueous medium, and in non-polar media. We herein review the physico-chemical properties of this class of compounds, with particular emphasis on the fluorescence emission properties of their neutral and/or ionic species, which has led to their widespread use as fluorescent probes in enzymology, including enzymes involved in purine metabolism, agonists/antagonists of adenosine receptors, mechanisms of catalytic RNAs, RNA editing, etc. They are also exceptionally useful fluorescent probes for analytical and clinical applications in crude cell homogenates.
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Affiliation(s)
- Jacek Wierzchowski
- Department of Biophysics, University of Varmia & Masuria, Oczapowskiego 4, 10-719 Olsztyn, Poland.
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20
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Cloning, Characterization and Bioinformatics Analysis of Novel Cytosine Deaminase from Escherichia coli AGH09. Int J Pept Res Ther 2015. [DOI: 10.1007/s10989-015-9465-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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21
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Manta B, Raushel FM, Himo F. Reaction Mechanism of Zinc-Dependent Cytosine Deaminase from Escherichia coli: A Quantum-Chemical Study. J Phys Chem B 2014; 118:5644-52. [DOI: 10.1021/jp501228s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bianca Manta
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
| | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
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22
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Trautwein-Schult A, Jankowska D, Cordes A, Hoferichter P, Klein C, Matros A, Mock HP, Baronian K, Bode R, Kunze G. Arxula adeninivorans recombinant guanine deaminase and its application in the production of food with low purine content. J Mol Microbiol Biotechnol 2014; 24:67-81. [PMID: 24481069 DOI: 10.1159/000357674] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/29/2013] [Indexed: 11/19/2022] Open
Abstract
Purines of exogenous and endogenous sources are degraded to uric acid in human beings. Concentrations >6.8 mg uric acid/dl serum cause hyperuricemia and its symptoms. Pharmaceuticals and the reduction of the intake of purine-rich food are used to control uric acid levels. A novel approach to the latter proposition is the enzymatic reduction of the purine content of food by purine-degrading enzymes. Here we describe the production of recombinant guanine deaminase by the yeast Arxula adeninivorans LS3 and its application in food. In media supplemented with nitrogen sources hypoxanthine or adenine, guanine deaminase (AGDA) gene expression is induced and intracellular accumulation of guanine deaminase (Agdap) protein occurs. The characteristics of the guanine deaminase isolated from wild-type strain LS3 and a transgenic strain expressing the AGDA gene under control of the strong constitutive TEF1 promoter were determined and compared. Both enzymes were dimeric and had temperature optima of 55°C with high substrate specificity for guanine and localisation in both the cytoplasm and vacuole of yeast. The enzyme was demonstrated to reduce levels of guanine in food. A mixture of guanine deaminase and other purine degradation enzymes will allow the reduction of purines in purine-rich foods.
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Affiliation(s)
- Anke Trautwein-Schult
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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23
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ZHANG XIN, LEI MING. WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.
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Affiliation(s)
- XIN ZHANG
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, P. R. China
- College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - MING LEI
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, P. R. China
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24
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Bitra A, Biswas A, Anand R. Structural Basis of the Substrate Specificity of Cytidine Deaminase Superfamily Guanine Deaminase. Biochemistry 2013; 52:8106-14. [DOI: 10.1021/bi400818e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Aruna Bitra
- Department of Chemistry, Indian Institute of Technology, Mumbai 400076, India
| | - Anwesha Biswas
- Department of Chemistry, Indian Institute of Technology, Mumbai 400076, India
| | - Ruchi Anand
- Department of Chemistry, Indian Institute of Technology, Mumbai 400076, India
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25
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Bitra A, Hussain B, Tanwar AS, Anand R. Identification of Function and Mechanistic Insights of Guanine Deaminase from Nitrosomonas europaea: Role of the C-Terminal Loop in Catalysis. Biochemistry 2013; 52:3512-22. [DOI: 10.1021/bi400068g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Aruna Bitra
- Department of Chemistry, IIT Bombay, Mumbai, India 400076
| | - Bhukya Hussain
- Department of Chemistry, IIT Bombay, Mumbai, India 400076
| | | | - Ruchi Anand
- Department of Chemistry, IIT Bombay, Mumbai, India 400076
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26
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Chen SC, Shen CY, Yen TM, Yu HC, Chang TH, Lai WL, Liaw SH. Evolution of vitamin B2biosynthesis: eubacterial RibG and fungal Rib2 deaminases. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:227-36. [DOI: 10.1107/s0907444912044903] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2012] [Accepted: 10/30/2012] [Indexed: 12/27/2022]
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27
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Investigations into specificity of azepinomycin for inhibition of guanase: discrimination between the natural heterocyclic inhibitor and its synthetic nucleoside analogues. Bioorg Med Chem Lett 2012; 22:7214-8. [PMID: 23084905 DOI: 10.1016/j.bmcl.2012.09.053] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/11/2012] [Accepted: 09/17/2012] [Indexed: 01/05/2023]
Abstract
In our long and broad program to explore structure-activity relationships of the natural product azepinomycin and its analogues for inhibition of guanase, an important enzyme of purine salvage pathway of nucleic acid metabolism, it became necessary to investigate if the nucleoside analogues of the heterocycle azepinomycin, which are likely to be formed in vivo, would be more or less potent than the parent heterocycle. To this end, we have resynthesized both azepinomycin (1) and its two diastereomeric nucleoside analogues (2 and 3), employing a modified, more efficient procedure, and have biochemically screened all three compounds against a mammalian guanase. Our results indicate that the natural product is at least 200 times more potent toward inhibition of guanase as compared with its nucleoside analogues, with the observed K(i) of azepinomycin (1) against the rabbit liver guanase=2.5 (±0.6)×10(-6) M, while K(i) of Compound 2=1.19 (±0.02)×10(-4) M and that of Compound 3=1.29 (±0.03)×10(-4) M. It is also to be noted that while IC(50) value of azepinomycin against guanase in cell culture has long been reported, no inhibition studies nor K(i) against a pure mammalian enzyme have ever been documented. In addition, we have, for the first time, determined the absolute stereochemistry of the 6-OH group of 2 and 3 using conformational analysis coupled with 2-D (1)H NMR NOESY.
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28
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Lin LYC, Rakic B, Chiu CPC, Lameignere E, Wakarchuk WW, Withers SG, Strynadka NCJ. Structure and mechanism of the lipooligosaccharide sialyltransferase from Neisseria meningitidis. J Biol Chem 2011; 286:37237-48. [PMID: 21880735 DOI: 10.1074/jbc.m111.249920] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The first x-ray crystallographic structure of a CAZY family-52 glycosyltransferase, that of the membrane associated α2,3/α2,6 lipooligosaccharide sialyltransferase from Neisseria meningitidis serotype L1 (NST), has been solved to 1.95 Å resolution. The structure of NST adopts a GT-B-fold common with other glycosyltransferase (GT) families but exhibits a novel domain swap of the N-terminal 130 residues to create a functional homodimeric form not observed in any other class to date. The domain swap is mediated at the structural level by a loop-helix-loop extension between residues Leu-108 and Met-130 (we term the swapping module) and a unique lipid-binding domain. NST catalyzes the creation of α2,3- or 2,6-linked oligosaccharide products from a CMP-sialic acid (Neu5Ac) donor and galactosyl-containing acceptor sugars. Our structures of NST bound to the non-hydrolyzable substrate analog CMP-3F((axial))-Neu5Ac show that the swapping module from one monomer of NST mediates the binding of the donor sugar in a composite active site formed at the dimeric interface. Kinetic analysis of designed point mutations observed in the CMP-3F((axial))-Neu5Ac binding site suggests potential roles of a requisite general base (Asp-258) and general acid (His-280) in the NST catalytic mechanism. A long hydrophobic tunnel adjacent to the dimer interface in each of the two monomers contains electron density for two extended linear molecules that likely belong to either the two fatty acyl chains of a diglyceride lipid or the two polyethylene glycol groups of the detergent Triton X-100. In this work, Triton X-100 maintains the activity and increases the solubility of NST during purification and is critical to the formation of ordered crystals. Together, the mechanistic implications of the NST structure provide insight into lipooligosaccharide sialylation with respect to the association of substrates and the essential membrane-anchored nature of NST on the bacterial surface.
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Affiliation(s)
- Leo Y-C Lin
- Department of Biochemistry and Molecular Biology, Centre for Blood Research University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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29
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Chakraborty S, Shah NH, Fishbein JC, Hosmane RS. A novel transition state analog inhibitor of guanase based on azepinomycin ring structure: Synthesis and biochemical assessment of enzyme inhibition. Bioorg Med Chem Lett 2011; 21:756-9. [PMID: 21183343 PMCID: PMC3035156 DOI: 10.1016/j.bmcl.2010.11.109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Revised: 11/21/2010] [Accepted: 11/23/2010] [Indexed: 11/27/2022]
Abstract
Synthesis and biochemical inhibition studies of a novel transition state analog inhibitor of guanase bearing the ring structure of azepinomycin have been reported. The compound was synthesized in five-steps from a known compound and biochemically screened against the rabbit liver guanase. The compound exhibited competitive inhibition profile with a K(i) of 16.7±0.5μM.
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Affiliation(s)
- Saibal Chakraborty
- Laboratory for Drug Design & Synthesis, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland, 21250, USA
| | - Niti H. Shah
- Laboratory for Drug Design & Synthesis, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland, 21250, USA
| | - James C. Fishbein
- Laboratory for Drug Design & Synthesis, Department of Chemistry & Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland, 21250, USA
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30
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Fernández JR, Sweet ES, Welsh WJ, Firestein BL. Identification of small molecule compounds with higher binding affinity to guanine deaminase (cypin) than guanine. Bioorg Med Chem 2010; 18:6748-55. [PMID: 20716488 DOI: 10.1016/j.bmc.2010.07.054] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/15/2010] [Accepted: 07/22/2010] [Indexed: 10/19/2022]
Abstract
Guanine deaminase (GDA; cypin) is an important metalloenzyme that processes the first step in purine catabolism, converting guanine to xanthine by hydrolytic deamination. In higher eukaryotes, GDA also plays an important role in the development of neuronal morphology by regulating dendritic arborization. In addition to its role in the maturing brain, GDA is thought to be involved in proper liver function since increased levels of GDA activity have been correlated with liver disease and transplant rejection. Although mammalian GDA is an attractive and potential drug target for treatment of both liver diseases and cognitive disorders, prospective novel inhibitors and/or activators of this enzyme have not been actively pursued. In this study, we employed the combination of protein structure analysis and experimental kinetic studies to seek novel potential ligands for human guanine deaminase. Using virtual screening and biochemical analysis, we identified common small molecule compounds that demonstrate a higher binding affinity to GDA than does guanine. In vitro analysis demonstrates that these compounds inhibit guanine deamination, and more surprisingly, affect GDA (cypin)-mediated microtubule assembly. The results in this study provide evidence that an in silico drug discovery strategy coupled with in vitro validation assays can be successfully implemented to discover compounds that may possess therapeutic value for the treatment of diseases and disorders where GDA activity is abnormal.
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Affiliation(s)
- José R Fernández
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, 604 Allison Road, Piscataway, NJ 08854-8082, USA
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31
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Kim J, Park SI, Ahn C, Kim H, Yim J. Guanine deaminase functions as dihydropterin deaminase in the biosynthesis of aurodrosopterin, a minor red eye pigment of Drosophila. J Biol Chem 2009; 284:23426-35. [PMID: 19567870 DOI: 10.1074/jbc.m109.016493] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dihydropterin deaminase, which catalyzes the conversion of 7,8-dihydropterin to 7,8-dihydrolumazine, was purified 5850-fold to apparent homogeneity from Drosophila melanogaster. Its molecular mass was estimated to be 48 kDa by gel filtration and SDS-PAGE, indicating that it is a monomer under native conditions. The pI value, temperature, and optimal pH of the enzyme were 5.5, 40 degrees C, and 7.5, respectively. Interestingly the enzyme had much higher activity for guanine than for 7,8-dihydropterin. The specificity constant (k(cat)/K(m)) for guanine (8.6 x 10(6) m(-1).s(-1)) was 860-fold higher than that for 7,8-dihydropterin (1.0 x 10(4) m(-1).s(-1)). The structural gene of the enzyme was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis as CG18143, located at region 82A1 on chromosome 3R. The cloned and expressed CG18143 exhibited both 7,8-dihydropterin and guanine deaminase activities. Flies with mutations in CG18143, SUPor-P/Df(3R)A321R1 transheterozygotes, had severely decreased activities in both deaminases compared with the wild type. Among several red eye pigments, the level of aurodrosopterin was specifically decreased in the mutant, and the amount of xanthine and uric acid also decreased considerably to 76 and 59% of the amounts in the wild type, respectively. In conclusion, dihydropterin deaminase encoded by CG18143 plays a role in the biosynthesis of aurodrosopterin by providing one of its precursors, 7,8-dihydrolumazine, from 7,8-dihydropterin. Dihydropterin deaminase also functions as guanine deaminase, an important enzyme for purine metabolism.
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Affiliation(s)
- Jaekwang Kim
- School of Biological Sciences, Seoul National University, Seoul 151-742, Korea
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32
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Fernández JR, Byrne B, Firestein BL. Phylogenetic analysis and molecular evolution of guanine deaminases: from guanine to dendrites. J Mol Evol 2009; 68:227-35. [PMID: 19221682 DOI: 10.1007/s00239-009-9205-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Revised: 10/30/2008] [Accepted: 01/21/2009] [Indexed: 01/02/2023]
Abstract
Guanine deaminase (GDA; guanase) is a ubiquitous enzyme that catalyzes the first step of purine metabolism by hydrolytic deamination of guanine, resulting in the production of xanthine. This hydrolase subfamily member plays an essential role in maintaining homeostasis of cellular triphosphate nucleotides for energy, signal transduction pathways, and nitrogen sources. In mammals, GDA protein levels can play a role in neuronal development by regulating dendritic arborization. We previously demonstrated that the most abundant alternative splice form of GDA in mammals, termed cypin (cytosolic PSD-95 interactor), interacts with postsynaptic density proteins, regulates microtubule polymerization, and increases dendrite number. Since purine metabolism and dendrite development were previously thought to be independent cellular processes, this multifunctional protein serves as a new target for the treatment of cognitive disorders characterized by aberrant neuronal morphology and purine metabolism. Although the enzymatic activity of GDA has been conserved during evolution from prokaryotes to higher eukaryotes, a detailed evolutionary assessment of the principal domains in GDA proteins has not yet been put forward. In this study, we perform a complete evolutionary analysis of the full-length sequences and the principal domains in guanine deaminases. Furthermore, we reconstruct the molecular phylogeny of guanine deaminases with neighbor-joining, maximum-likelihood, and UPGMA methods of phylogenetic inference. This study can act as a model whereby a universal housekeeping enzyme may be adapted to act also as a key regulator of a developmental process.
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Affiliation(s)
- José R Fernández
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Nelson Biological Laboratories, 604 Allison Road, Piscataway, NJ 08854-8082, USA
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33
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Hosmane RS. Chapter 2: Ring-Expanded (‘Fat‘) Purines and their Nucleoside/Nucleotide Analogues as Broad-Spectrum Therapeutics. PROGRESS IN HETEROCYCLIC CHEMISTRY 2009; 21. [PMCID: PMC7147839 DOI: 10.1016/s0959-6380(09)70029-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
This chapter describes a family of ring-expanded purines, informally referred to as “fat” or f-purines, as well as their nucleoside/nucleotide analogues (RENs/RENTs) that have broad applications in chemistry, biology, and medicine. Although purine itself has never been found in nature, substituted purines, such as adenine and guanine, or their respective nucleoside derivatives, adenosine and guanosine, are the most ubiquitous class of nitrogen heterocycles and play crucial roles in wide variety of functions of living beings As nucleotides (AMP,GMP), they are the building blocks of nucleic acids (RNA/DNA). They serve as energy cofactors (ATP, GTP), as part of coenzymes (NAD/FAD) in oxidation-reduction reactions, as important second messengers in many intracellular signal transduction processes (cAMP/cGMP), or as direct neurotransmitters by binding to purinergic receptors (adenosine receptors). Therefore, it is not surprising that the analogues of purines have found utility both as chemotherapeutics (antiviral, antibiotic, and anticancer agents) and pharmacodynamic entities (the regulation of myocardial oxygen consumption and cardiac blood flow). While they can act as substrates or the inhibitors of the enzymes of purine metabolism to render their chemotherapeutic action, their ability to act as agonists or antagonists of A1/A2A receptors is the basis for the modulation of pharmacodynamic property.
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Chen SC, Lin YH, Yu HC, Liaw SH. Complex Structure of Bacillus subtilis RibG. J Biol Chem 2009; 284:1725-31. [DOI: 10.1074/jbc.m805820200] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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Médici R, Lewkowicz ES, Iribarren AM. Arthrobacter oxydansas a biocatalyst for purine deamination. FEMS Microbiol Lett 2008; 289:20-6. [DOI: 10.1111/j.1574-6968.2008.01349.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Tyagi R, Eswaramoorthy S, Burley SK, Raushel FM, Swaminathan S. A common catalytic mechanism for proteins of the HutI family. Biochemistry 2008; 47:5608-15. [PMID: 18442260 DOI: 10.1021/bi800180g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Imidazolonepropionase (HutI) (imidazolone-5-propanote hydrolase, EC 3.5.2.7) is a member of the amidohydrolase superfamily and catalyzes the conversion of imidazolone-5-propanoate to N-formimino-L-glutamate in the histidine degradation pathway. We have determined the three-dimensional crystal structures of HutI from Agrobacterium tumefaciens (At-HutI) and an environmental sample from the Sargasso Sea Ocean Going Survey (Es-HutI) bound to the product [ N-formimino-L-glutamate (NIG)] and an inhibitor [3-(2,5-dioxoimidazolidin-4-yl)propionic acid (DIP)], respectively. In both structures, the active site is contained within each monomer, and its organization displays the landmark feature of the amidohydrolase superfamily, showing a metal ligand (iron), four histidines, and one aspartic acid. A catalytic mechanism involving His265 is proposed on the basis of the inhibitor-bound structure. This mechanism is applicable to all HutI forms.
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Affiliation(s)
- Rajiv Tyagi
- Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA
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Fernández JR, Welsh WJ, Firestein BL. Structural characterization of the zinc binding domain in cytosolic PSD-95 interactor (cypin): Role of zinc binding in guanine deamination and dendrite branching. Proteins 2008; 70:873-81. [PMID: 17803218 PMCID: PMC2721013 DOI: 10.1002/prot.21683] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Dendrite morphology regulates how a postsynaptic neuron receives information from presynaptic neurons. The specific patterning of dendrite branches is promoted by extrinsic and intrinsic factors that trigger the activation of functional signaling pathways. However, most of the regulating factors and the biochemical mechanisms involved in regulating dendrite branching are unknown. Our laboratory previously reported that cypin (cytosolic PSD-95 interactor) plays an active role in regulating dendrite branching in hippocampal neurons. Cypin-promoted increases in dendrite number are dependent on guanine deaminase activity. In order to identify the specific structural role of zinc-binding in cypin-mediated dendrite branching and guanine deaminase activity, we employed computational homology modeling techniques to construct a three dimensional structural model of cypin. Analysis of the protein-ion sequestration scaffold of this model identified several histidines and aspartic acid residues responsible for zinc binding. Single substitution mutations in these specific sites completely disrupted the guanine deaminase enzymatic activity and rendered cypin unable to promote dendrite branching in rat hippocampal neurons. The specific zinc ion-binding function of each residue in the protein scaffold was also confirmed by Inductively Coupled Plasma-Optic Emission Spectrometry. Inspection of our structural model confirmed that His82 and His84 coordinate with the zinc ion, together with His240, His279, and Asp330, residues that until now were unknown to play a role in this regard. Furthermore, promotion of dendrite branching by cypin is zinc-dependent.
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Affiliation(s)
- José R. Fernández
- Department of Cell Biology and Neuroscience, Rutgers University, 604 Allison Road, Piscataway, New Jersey 08854-8082
- Molecular Biosciences Graduate Program, Rutgers University, 604 Allison Road, Piscataway, New Jersey 08854-8082
| | - William J. Welsh
- Department of Pharmacology, University of Medicine and Dentistry of New Jersey (UMDNJ), Robert Wood Johnson Medical School and UMDNJ Informatics Institute, Piscataway, New Jersey 08854
| | - Bonnie L. Firestein
- Department of Cell Biology and Neuroscience, Rutgers University, 604 Allison Road, Piscataway, New Jersey 08854-8082
- Correspondence to: Bonnie L. Firestein, Department of Cell Biology and Neuroscience, Rutgers, the State University of New Jersey, Nelson Biological Laboratories, 604 Allison Road, Piscataway, NJ 08854-8082. E-mail:
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Yao L, Cukier RI, Yan H. Catalytic mechanism of guanine deaminase: an ONIOM and molecular dynamics study. J Phys Chem B 2007; 111:4200-10. [PMID: 17394305 DOI: 10.1021/jp0673056] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The catalytic mechanism of Bacillus subtilis guanine deaminase (bGD), a Zn metalloenzyme, has been investigated by a combination of quantum mechanical calculations using the multilayered ONIOM method and molecular dynamics simulations. In contrast to a previously proposed catalytic mechanism, which requires the bound guanine to assume a rare tautomeric state, the ONIOM calculations showed that the active-site residues of the enzyme do not affect the tautomeric state of guanine, and consequently the bound guanine is a tautomer that is the most abundant in aqueous solution. Two residues, Glutamate 55 and Aspartate 114, were found to play important roles in proton shuttling in the reaction. The proposed reaction path is initiated by proton transfer from a Zn-bound water to protonate Asp114. This process may be quite complex and rather dynamic in nature, as revealed by the molecular dynamics (MD) simulations, whereby another water may bridge the Zn-bound water and Asp114, which then is eliminated by positioning of guanine in the active site. The binding of guanine stabilizes protonated Asp114 by hydrogen bond formation. Asp114 can then transfer its proton to the N3 of the bound guanine, facilitating the nucleophilic attack on C2 of the guanine by the Zn-bound hydroxide to form a tetrahedral intermediate. This occurs with a rather low barrier. Glu55 then transfers a proton from the Zn-hydroxide to the amino group of the reaction intermediate and, at this point, the C2-N2 bond has lengthened by 0.2 A compared to guanine, making C2-N2 bond cleavage more facile. The C2-N2 bond breaks forming ammonia, with an energy barrier of approximately 8.8 kcal/mol. Ammonia leaves the active site, and xanthine is freed by the cleavage of the Zn-O2 bond, with a barrier approximately 8.4 kcal/mol. Along this reaction path, the highest barrier comes from C2-N2 bond cleavage, while the barrier from the cleavage of the Zn-O2 bond is slightly smaller. The Zn-O2 bond can be broken without the assistance of water during the release of xanthine.
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Affiliation(s)
- Lishan Yao
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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Ujjinamatada RK, Bhan A, Hosmane RS. Design of inhibitors against guanase: Synthesis and biochemical evaluation of analogues of azepinomycin. Bioorg Med Chem Lett 2006; 16:5551-4. [PMID: 16920357 DOI: 10.1016/j.bmcl.2006.08.033] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2006] [Revised: 08/04/2006] [Accepted: 08/07/2006] [Indexed: 10/24/2022]
Abstract
As part of a program to design rational, mechanism-based inhibitors of guanase, we report here the synthesis and biochemical screening of two analogues of azepinomycin (1 and 2), a naturally occurring inhibitor of guanase, known to mimic the transition-state of the enzyme-catalyzed reaction. Our biochemical results show that compounds 1 and 2 are competitive inhibitors with K(i) of 2.01+/-0.16 x 10(-5) and 5.36+/-0.14 x 10(-5) M, respectively.
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Affiliation(s)
- Ravi K Ujjinamatada
- Laboratory for Drug Design and Synthesis, Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
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Chen SC, Chang YC, Lin CH, Lin CH, Liaw SH. Crystal structure of a bifunctional deaminase and reductase from Bacillus subtilis involved in riboflavin biosynthesis. J Biol Chem 2005; 281:7605-13. [PMID: 16308316 DOI: 10.1074/jbc.m510254200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bacterial RibG is an attractive candidate for development of antimicrobial drugs because of its involvement in the riboflavin biosynthesis. The crystal structure of Bacillus subtilis RibG at 2.41-A resolution displayed a tetrameric ring-like structure with an extensive interface of approximately 2400 A(2)/monomer. The N-terminal deaminase domain belongs to the cytidine deaminase superfamily. A structure-based sequence alignment of a variety of nucleotide deaminases reveals not only the unique signatures in each family member for gene annotation but also putative substrate-interacting residues for RNA-editing deaminases. The strong structural conservation between the C-terminal reductase domain and the pharmaceutically important dihydrofolate reductase suggests that the two reductases involved in the riboflavin and folate biosyntheses evolved from a single ancestral gene. Together with the binding of the essential cofactors, zinc ion and NADPH, the structural comparison assists substrate modeling into the active-site cavities allowing identification of specific substrate recognition. Finally, the present structure reveals that the deaminase and the reductase are separate functional domains and that domain fusion is crucial for the enzyme activities through formation of a stable tetrameric structure.
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Affiliation(s)
- Sheng-Chia Chen
- Structural Biology Program, Institute of Biochemistry, and Faculty of Life Science, National Yang-Ming University, Taipei 11221, Taiwan
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Kuratani M, Ishii R, Bessho Y, Fukunaga R, Sengoku T, Shirouzu M, Sekine SI, Yokoyama S. Crystal structure of tRNA adenosine deaminase (TadA) from Aquifex aeolicus. J Biol Chem 2005; 280:16002-8. [PMID: 15677468 DOI: 10.1074/jbc.m414541200] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The bacterial tRNA adenosine deaminase (TadA) generates inosine by deaminating the adenosine residue at the wobble position of tRNA(Arg-2). This modification is essential for the decoding system. In this study, we determined the crystal structure of Aquifex aeolicus TadA at a 1.8-A resolution. This is the first structure of a deaminase acting on tRNA. A. aeolicus TadA has an alpha/beta/alpha three-layered fold and forms a homodimer. The A. aeolicus TadA dimeric structure is completely different from the tetrameric structure of yeast CDD1, which deaminates mRNA and cytidine, but is similar to the dimeric structure of yeast cytosine deaminase. However, in the A. aeolicus TadA structure, the shapes of the C-terminal helix and the regions between the beta4 and beta5 strands are quite distinct from those of yeast cytosine deaminase and a large cavity is produced. This cavity contains many conserved amino acid residues that are likely to be involved in either catalysis or tRNA binding. We made a docking model of TadA with the tRNA anticodon stem loop.
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Affiliation(s)
- Mitsuo Kuratani
- Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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