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Hung SH, Elliott GI, Ramkumar TR, Burtnyak L, McGrenaghan CJ, Alkuzweny S, Quaiyum S, Iwata-Reuyl D, Pan X, Green BD, Kelly VP, de Crécy-Lagard V, Swairjo M. Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5'-monophosphate as the biological substrate. Nucleic Acids Res 2023; 51:935-951. [PMID: 36610787 PMCID: PMC9881137 DOI: 10.1093/nar/gkac1231] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 01/09/2023] Open
Abstract
Eukaryotic life benefits from-and ofttimes critically relies upon-the de novo biosynthesis and supply of vitamins and micronutrients from bacteria. The micronutrient queuosine (Q), derived from diet and/or the gut microbiome, is used as a source of the nucleobase queuine, which once incorporated into the anticodon of tRNA contributes to translational efficiency and accuracy. Here, we report high-resolution, substrate-bound crystal structures of the Sphaerobacter thermophilus queuine salvage protein Qng1 (formerly DUF2419) and of its human ortholog QNG1 (C9orf64), which together with biochemical and genetic evidence demonstrate its function as the hydrolase releasing queuine from queuosine-5'-monophosphate as the biological substrate. We also show that QNG1 is highly expressed in the liver, with implications for Q salvage and recycling. The essential role of this family of hydrolases in supplying queuine in eukaryotes places it at the nexus of numerous (patho)physiological processes associated with queuine deficiency, including altered metabolism, proliferation, differentiation and cancer progression.
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Affiliation(s)
- Shr-Hau Hung
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
- The Viral Information Institute, San Diego State University, San Diego, CA, USA
| | - Gregory I Elliott
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
| | - Thakku R Ramkumar
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Lyubomyr Burtnyak
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Callum J McGrenaghan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Sana Alkuzweny
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
| | - Samia Quaiyum
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
| | - Dirk Iwata-Reuyl
- Department of Chemistry, PO Box 751 Portland State University, Portland, OR 97207, USA
| | - Xiaobei Pan
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Brian D Green
- School of Biological Sciences, Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - Vincent P Kelly
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA
- University of Florida Genetics Institute, Gainesville, FL 32610, USA
| | - Manal A Swairjo
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA, USA
- The Viral Information Institute, San Diego State University, San Diego, CA, USA
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Zhang WH, Wang F, Wang YL, You S, Pan HX, Tang GL. Identification and Characterization of Enzymes Catalyzing Early Steps in Miharamycin and Amipurimycin Biosynthesis. Org Lett 2021; 23:8761-8765. [PMID: 34747180 DOI: 10.1021/acs.orglett.1c03254] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The biochemical elucidation of the early biosynthetic pathways of miharamycins and amipurimycin revealed the roles of several enzymes, which include GMP hydrolase, represented by MihD/ApmD, and hypothetical proteins, MihI/ApmI, unexpectedly exhibiting the dual function of the guanylglucuronic acid assembly and GMP cleavage. In addition, MihE, a carbonyl reductase that functions on the C2 branch of high-carbon sugars, and MihF, a rare guanine O-methyltransferase, were also functionally verified.
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Affiliation(s)
- Wen-He Zhang
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Fei Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
| | - Yi-Lin Wang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
| | - Song You
- School of Life Sciences and Biopharmaceuticals, Shenyang Pharmaceutical University, Benxi 117004, China
| | - Hai-Xue Pan
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of CAS, CAS, Shanghai 200032, China
| | - Gong-Li Tang
- School of Chemistry and Materials Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences (CAS), Hangzhou 310024, China
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, University of CAS, CAS, Shanghai 200032, China
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Kang M, Doddapaneni K, Sarni S, Heppner Z, Wysocki V, Wu Z. Solution structure of the nucleotide hydrolase BlsM: Implication of its substrate specificity. Protein Sci 2021; 29:1760-1773. [PMID: 31876335 DOI: 10.1002/pro.3812] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 12/17/2019] [Accepted: 12/21/2019] [Indexed: 11/06/2022]
Abstract
Biosynthesis of the peptidyl nucleoside antifungal agent blasticidin S in Streptomyces griseochromogenes requires the hydrolytic function of a nucleotide hydrolase, BlsM, to excise the free cytosine from the 5'-monophosphate cytosine nucleotide. In addition to its hydrolytic activity, interestingly, BlsM has also been shown to possess a novel cytidine deaminase activity, converting cytidine, and deoxycytidine to uridine and deoxyuridine. To gain insight into the substrate specificity of BlsM and the mechanism by which it performs these dual function, the solution structure of BlsM was determined by multi-dimensional nuclear magnetic resonance approaches. BlsM displays a nucleoside deoxyribosyltransferase-like dimeric topology, with each monomer consisting of a five-stranded β-sheet that is sandwiched by five α-helixes. Compared with the purine nucleotide hydrolase RCL, each monomer of BlsM has a smaller active site pocket, enclosed by a group of conserved hydrophobic residues from both monomers. The smaller size of active site is consistent with its substrate specificity for a pyrimidine, whereas a much more open active site, as in RCL might be required to accommodate a larger purine ring. In addition, BlsM confers its substrate specificity for a ribosyl-nucleotide through a key residue, Phe19. When mutated to a tyrosine, F19Y reverses its substrate preference. While significantly impaired in its hydrolytic capability, F19Y exhibited a pronounced deaminase activity on CMP, presumably due to an altered substrate orientation as a result of a steric clash between the 2'-hydroxyl of CMP and the ζ-OH group of F19Y. Finally, Glu105 appears to be critical for the dual function of BlsM.
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Affiliation(s)
- Minhee Kang
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Kiran Doddapaneni
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Samantha Sarni
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Zach Heppner
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Vicki Wysocki
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
| | - Zhengrong Wu
- Chemistry and Biochemistry Department, Ohio State University, Columbus, Ohio
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