1
|
Shan Z, Rivero-Gamez A, Lyumkis D, Horton NC. Two-metal ion mechanism of DNA cleavage by activated, filamentous SgrAI. J Biol Chem 2024; 300:107576. [PMID: 39009341 PMCID: PMC11367474 DOI: 10.1016/j.jbc.2024.107576] [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: 05/03/2024] [Revised: 06/21/2024] [Accepted: 07/09/2024] [Indexed: 07/17/2024] Open
Abstract
Enzymes that form filamentous assemblies with modulated enzymatic activities have gained increasing attention in recent years. SgrAI is a sequence specific type II restriction endonuclease that forms polymeric filaments with accelerated DNA cleavage activity and expanded DNA sequence specificity. Prior studies have suggested a mechanistic model linking the structural changes accompanying SgrAI filamentation to its accelerated DNA cleavage activity. In this model, the conformational changes that are specific to filamentous SgrAI maximize contacts between different copies of the enzyme within the filament and create a second divalent cation binding site in each subunit, which in turn facilitates the DNA cleavage reaction. However, our understanding of the atomic mechanism of catalysis is incomplete. Herein, we present two new structures of filamentous SgrAI solved using cryo-EM. The first structure, resolved to 3.3 Å, is of filamentous SgrAI containing an active site mutation that is designed to stall the DNA cleavage reaction, which reveals the enzymatic configuration prior to DNA cleavage. The second structure, resolved to 3.1 Å, is of WT filamentous SgrAI containing cleaved substrate DNA, which reveals the enzymatic configuration at the end of the enzymatic cleavage reaction. Both structures contain the phosphate moiety at the cleavage site and the biologically relevant divalent cation cofactor Mg2+ and define how the Mg2+ cation reconfigures during enzymatic catalysis. The data support a model for the activation mechanism that involves binding of a second Mg2+ in the SgrAI active site as a direct result of filamentation induced conformational changes.
Collapse
Affiliation(s)
- Zelin Shan
- The Salk Institute of Biological Sciences, La Jolla, California, USA
| | - Andres Rivero-Gamez
- The Salk Institute of Biological Sciences, La Jolla, California, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego La Jolla, California, USA
| | - Dmitry Lyumkis
- The Salk Institute of Biological Sciences, La Jolla, California, USA; Department of Molecular Biology, School of Biological Sciences, University of California, San Diego La Jolla, California, USA.
| | - Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA.
| |
Collapse
|
2
|
Horton JR, Borgaro JG, Griggs RM, Quimby A, Guan S, Zhang X, Wilson GG, Zheng Y, Zhu Z, Cheng X. Structure of 5-hydroxymethylcytosine-specific restriction enzyme, AbaSI, in complex with DNA. Nucleic Acids Res 2014; 42:7947-59. [PMID: 24895434 PMCID: PMC4081097 DOI: 10.1093/nar/gku497] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AbaSI, a member of the PvuRts1I-family of modification-dependent restriction endonucleases, cleaves deoxyribonucleic acid (DNA) containing 5-hydroxymethylctosine (5hmC) and glucosylated 5hmC (g5hmC), but not DNA containing unmodified cytosine. AbaSI has been used as a tool for mapping the genomic locations of 5hmC, an important epigenetic modification in the DNA of higher organisms. Here we report the crystal structures of AbaSI in the presence and absence of DNA. These structures provide considerable, although incomplete, insight into how this enzyme acts. AbaSI appears to be mainly a homodimer in solution, but interacts with DNA in our structures as a homotetramer. Each AbaSI subunit comprises an N-terminal, Vsr-like, cleavage domain containing a single catalytic site, and a C-terminal, SRA-like, 5hmC-binding domain. Two N-terminal helices mediate most of the homodimer interface. Dimerization brings together the two catalytic sites required for double-strand cleavage, and separates the 5hmC binding-domains by ∼70 Å, consistent with the known activity of AbaSI which cleaves DNA optimally between symmetrically modified cytosines ∼22 bp apart. The eukaryotic SET and RING-associated (SRA) domains bind to DNA containing 5-methylcytosine (5mC) in the hemi-methylated CpG sequence. They make contacts in both the major and minor DNA grooves, and flip the modified cytosine out of the helix into a conserved binding pocket. In contrast, the SRA-like domain of AbaSI, which has no sequence specificity, contacts only the minor DNA groove, and in our current structures the 5hmC remains intra-helical. A conserved, binding pocket is nevertheless present in this domain, suitable for accommodating 5hmC and g5hmC. We consider it likely, therefore, that base-flipping is part of the recognition and cleavage mechanism of AbaSI, but that our structures represent an earlier, pre-flipped stage, prior to actual recognition.
Collapse
Affiliation(s)
- John R Horton
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Janine G Borgaro
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Rose M Griggs
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | - Aine Quimby
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Shengxi Guan
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Xing Zhang
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| | | | - Yu Zheng
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Zhenyu Zhu
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Xiaodong Cheng
- Department of Biochemistry, Emory University School of Medicine, 1510 Clifton Road, Atlanta, Georgia 30322, USA
| |
Collapse
|
3
|
Xiao S, Klein ML, LeBard DN, Levine BG, Liang H, MacDermaid CM, Alfonso-Prieto M. Magnesium-Dependent RNA Binding to the PA Endonuclease Domain of the Avian Influenza Polymerase. J Phys Chem B 2014; 118:873-89. [DOI: 10.1021/jp408383g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Shiyan Xiao
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Michael L. Klein
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - David N. LeBard
- Department of Chemistry, Yeshiva University, New York, New York 10033, United States
| | - Benjamin G. Levine
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Haojun Liang
- CAS Key Laboratory of Soft Matter Chemistry, Department of Polymer Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Christopher M. MacDermaid
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Mercedes Alfonso-Prieto
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania 19122, United States
| |
Collapse
|
4
|
Ben-David M, Elias M, Filippi JJ, Duñach E, Silman I, Sussman JL, Tawfik DS. Catalytic versatility and backups in enzyme active sites: the case of serum paraoxonase 1. J Mol Biol 2012; 418:181-96. [PMID: 22387469 DOI: 10.1016/j.jmb.2012.02.042] [Citation(s) in RCA: 128] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 02/19/2012] [Accepted: 02/22/2012] [Indexed: 12/15/2022]
Abstract
The origins of enzyme specificity are well established. However, the molecular details underlying the ability of a single active site to promiscuously bind different substrates and catalyze different reactions remain largely unknown. To better understand the molecular basis of enzyme promiscuity, we studied the mammalian serum paraoxonase 1 (PON1) whose native substrates are lipophilic lactones. We describe the crystal structures of PON1 at a catalytically relevant pH and of its complex with a lactone analogue. The various PON1 structures and the analysis of active-site mutants guided the generation of docking models of the various substrates and their reaction intermediates. The models suggest that promiscuity is driven by coincidental overlaps between the reactive intermediate for the native lactonase reaction and the ground and/or intermediate states of the promiscuous reactions. This overlap is also enabled by different active-site conformations: the lactonase activity utilizes one active-site conformation whereas the promiscuous phosphotriesterase activity utilizes another. The hydrolysis of phosphotriesters, and of the aromatic lactone dihydrocoumarin, is also driven by an alternative catalytic mode that uses only a subset of the active-site residues utilized for lactone hydrolysis. Indeed, PON1's active site shows a remarkable level of networking and versatility whereby multiple residues share the same task and individual active-site residues perform multiple tasks (e.g., binding the catalytic calcium and activating the hydrolytic water). Overall, the coexistence of multiple conformations and alternative catalytic modes within the same active site underlines PON1's promiscuity and evolutionary potential.
Collapse
Affiliation(s)
- Moshe Ben-David
- Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | | | | | | | | | | | | |
Collapse
|
5
|
Firczuk M, Wojciechowski M, Czapinska H, Bochtler M. DNA intercalation without flipping in the specific ThaI-DNA complex. Nucleic Acids Res 2010; 39:744-54. [PMID: 20861000 PMCID: PMC3025569 DOI: 10.1093/nar/gkq834] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
The PD-(D/E)XK type II restriction endonuclease ThaI cuts the target sequence CG/CG with blunt ends. Here, we report the 1.3 Å resolution structure of the enzyme in complex with substrate DNA and a sodium or calcium ion taking the place of a catalytic magnesium ion. The structure identifies Glu54, Asp82 and Lys93 as the active site residues. This agrees with earlier bioinformatic predictions and implies that the PD and (D/E)XK motifs in the sequence are incidental. DNA recognition is very unusual: the two Met47 residues of the ThaI dimer intercalate symmetrically into the CG steps of the target sequence. They approach the DNA from the minor groove side and penetrate the base stack entirely. The DNA accommodates the intercalating residues without nucleotide flipping by a doubling of the CG step rise to twice its usual value, which is accompanied by drastic unwinding. Displacement of the Met47 side chains from the base pair midlines toward the downstream CG steps leads to large and compensating tilts of the first and second CG steps. DNA intercalation by ThaI is unlike intercalation by HincII, HinP1I or proteins that bend or repair DNA.
Collapse
|