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Chang C, Zhou G, Gao Y. Observing one-divalent-metal-ion dependent and histidine-promoted His-Me family I-PpoI nuclease catalysis in crystallo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.02.592236. [PMID: 38746211 PMCID: PMC11092635 DOI: 10.1101/2024.05.02.592236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Metal-ion-dependent nucleases play crucial roles in cellular defense and biotechnological applications. Time-resolved crystallography has resolved catalytic details of metal-ion-dependent DNA hydrolysis and synthesis, uncovering the essential roles of multiple metal ions during catalysis. The histidine-metal (His-Me) superfamily nucleases are renowned for binding one divalent metal ion and requiring a conserved histidine to promote catalysis. Many His-Me family nucleases, including homing endonucleases and Cas9 nuclease, have been adapted for biotechnological and biomedical applications. However, it remains unclear how the single metal ion in His-Me nucleases, together with the histidine, promotes water deprotonation, nucleophilic attack, and phosphodiester bond breakage. By observing DNA hydrolysis in crystallo with His-Me I-PpoI nuclease as a model system, we proved that only one divalent metal ion is required during its catalysis. Moreover, we uncovered several possible deprotonation pathways for the nucleophilic water. Interestingly, binding of the single metal ion and water deprotonation are concerted during catalysis. Our results reveal catalytic details of His-Me nucleases, which is distinct from multi-metal-ion-dependent DNA polymerases and nucleases.
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Affiliation(s)
- Caleb Chang
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
| | - Grace Zhou
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, Texas, 77005, USA
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4
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Chang C, Zhou G, Lee Luo C, Eleraky S, Moradi M, Gao Y. Sugar ring alignment and dynamics underline cytarabine and gemcitabine inhibition on Pol η catalyzed DNA synthesis. J Biol Chem 2024; 300:107361. [PMID: 38735473 PMCID: PMC11176770 DOI: 10.1016/j.jbc.2024.107361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/14/2024] Open
Abstract
Nucleoside analogue drugs are pervasively used as antiviral and chemotherapy agents. Cytarabine and gemcitabine are anti-cancer nucleoside analogue drugs that contain C2' modifications on the sugar ring. Despite carrying all the required functional groups for DNA synthesis, these two compounds inhibit DNA extension once incorporated into DNA. It remains unclear how the C2' modifications on cytarabine and gemcitabine affect the polymerase active site during substrate binding and DNA extension. Using steady-state kinetics, static and time-resolved X-ray crystallography with DNA polymerase η (Pol η) as a model system, we showed that the sugar ring C2' chemical groups on cytarabine and gemcitabine snugly fit within the Pol η active site without occluding the steric gate. During DNA extension, Pol η can extend past gemcitabine but with much lower efficiency past cytarabine. The Pol η crystal structures show that the -OH modification in the β direction on cytarabine locks the sugar ring in an unfavorable C2'-endo geometry for product formation. On the other hand, the addition of fluorine atoms on gemcitabine alters the proper conformational transition of the sugar ring for DNA synthesis. Our study illustrates mechanistic insights into chemotherapeutic drug inhibition and resistance and guides future optimization of nucleoside analogue drugs.
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Affiliation(s)
- Caleb Chang
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Grace Zhou
- Department of Biosciences, Rice University, Houston, Texas, USA
| | | | - Sarah Eleraky
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Madeline Moradi
- Department of Biosciences, Rice University, Houston, Texas, USA
| | - Yang Gao
- Department of Biosciences, Rice University, Houston, Texas, USA.
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5
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Krishna R, Wang J, Ahern W, Sturmfels P, Venkatesh P, Kalvet I, Lee GR, Morey-Burrows FS, Anishchenko I, Humphreys IR, McHugh R, Vafeados D, Li X, Sutherland GA, Hitchcock A, Hunter CN, Kang A, Brackenbrough E, Bera AK, Baek M, DiMaio F, Baker D. Generalized biomolecular modeling and design with RoseTTAFold All-Atom. Science 2024; 384:eadl2528. [PMID: 38452047 DOI: 10.1126/science.adl2528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/27/2024] [Indexed: 03/09/2024]
Abstract
Deep-learning methods have revolutionized protein structure prediction and design but are presently limited to protein-only systems. We describe RoseTTAFold All-Atom (RFAA), which combines a residue-based representation of amino acids and DNA bases with an atomic representation of all other groups to model assemblies that contain proteins, nucleic acids, small molecules, metals, and covalent modifications, given their sequences and chemical structures. By fine-tuning on denoising tasks, we developed RFdiffusion All-Atom (RFdiffusionAA), which builds protein structures around small molecules. Starting from random distributions of amino acid residues surrounding target small molecules, we designed and experimentally validated, through crystallography and binding measurements, proteins that bind the cardiac disease therapeutic digoxigenin, the enzymatic cofactor heme, and the light-harvesting molecule bilin.
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Affiliation(s)
- Rohith Krishna
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Jue Wang
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Woody Ahern
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Pascal Sturmfels
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Preetham Venkatesh
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Indrek Kalvet
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | - Gyu Rie Lee
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
| | | | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ian R Humphreys
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Ryan McHugh
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Graduate Program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA
| | - Dionne Vafeados
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Xinting Li
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | | | - Andrew Hitchcock
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - C Neil Hunter
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
| | - Alex Kang
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Evans Brackenbrough
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Asim K Bera
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - Minkyung Baek
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, WA 98105, USA
- Institute for Protein Design, University of Washington, Seattle, WA 98105, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA
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6
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Lin G, Barnes CO, Weiss S, Dutagaci B, Qiu C, Feig M, Song J, Lyubimov A, Cohen AE, Kaplan CD, Calero G. Structural basis of transcription: RNA Polymerase II substrate binding and metal coordination at 3.0 Å using a free-electron laser. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.22.559052. [PMID: 37790421 PMCID: PMC10543002 DOI: 10.1101/2023.09.22.559052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Catalysis and translocation of multi-subunit DNA-directed RNA polymerases underlie all cellular mRNA synthesis. RNA polymerase II (Pol II) synthesizes eukaryotic pre-mRNAs from a DNA template strand buried in its active site. Structural details of catalysis at near atomic resolution and precise arrangement of key active site components have been elusive. Here we present the free electron laser (FEL) structure of a matched ATP-bound Pol II, revealing the full active site interaction network at the highest resolution to date, including the trigger loop (TL) in the closed conformation, bonafide occupancy of both site A and B Mg2+, and a putative third (site C) Mg2+ analogous to that described for some DNA polymerases but not observed previously for cellular RNA polymerases. Molecular dynamics (MD) simulations of the structure indicate that the third Mg2+ is coordinated and stabilized at its observed position. TL residues provide half of the substrate binding pocket while multiple TL/bridge helix (BH) interactions induce conformational changes that could propel translocation upon substrate hydrolysis. Consistent with TL/BH communication, a FEL structure and MD simulations of the hyperactive Rpb1 T834P bridge helix mutant reveals rearrangement of some active site interactions supporting potential plasticity in active site function and long-distance effects on both the width of the central channel and TL conformation, likely underlying its increased elongation rate at the expense of fidelity.
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Affiliation(s)
- Guowu Lin
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Christopher O Barnes
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena CA 91125 USA
| | - Simon Weiss
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
| | - Bercem Dutagaci
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Chenxi Qiu
- Department of Genetics, Harvard Medical School, Boston MA 02115 USA
| | - Michael Feig
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing MI 48824 USA
| | - Jihnu Song
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Artem Lyubimov
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh PA 15260 USA
| | - Guillermo Calero
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA 15261 USA
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9
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Weaver TM, Washington MT, Freudenthal BD. New insights into DNA polymerase mechanisms provided by time-lapse crystallography. Curr Opin Struct Biol 2022; 77:102465. [PMID: 36174287 PMCID: PMC9772199 DOI: 10.1016/j.sbi.2022.102465] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/15/2022] [Accepted: 08/24/2022] [Indexed: 12/24/2022]
Abstract
DNA polymerases play central roles in DNA replication and repair by catalyzing template-directed nucleotide incorporation. Recently time-lapse X-ray crystallography, which allows one to observe reaction intermediates, has revealed numerous and unexpected mechanistic features of DNA polymerases. In this article, we will examine recent new discoveries that have come from time-lapse crystallography that are currently transforming our understanding of the structural mechanisms used by DNA polymerases. Among these new discoveries are the binding of a third metal ion within the polymerase active site, the mechanisms of translocation along the DNA, the presence of new fidelity checkpoints, a novel pyrophosphatase activity within the active site, and the mechanisms of pyrophosphorolysis.
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Affiliation(s)
- Tyler M Weaver
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA. https://twitter.com/tylermweaver1
| | - M Todd Washington
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA.
| | - Bret D Freudenthal
- Department of Biochemistry and Molecular Biology, Department of Cancer Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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