1
|
Seo PW, Hofmann A, Kim JH, Hwangbo SA, Kim JH, Kim JW, Huynh TYL, Choy HE, Kim SJ, Lee J, Lee JO, Jin KS, Park SY, Kim JS. Structural features of a minimal intact methyltransferase of a type I restriction-modification system. Int J Biol Macromol 2022; 208:381-389. [PMID: 35337914 DOI: 10.1016/j.ijbiomac.2022.03.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/16/2022] [Accepted: 03/17/2022] [Indexed: 11/05/2022]
Abstract
Type I restriction-modification enzymes are oligomeric proteins composed of methylation (M), DNA sequence-recognition (S), and restriction (R) subunits. The different bipartite DNA sequences of 2-4 consecutive bases are recognized by two discerned target recognition domains (TRDs) located at the two-helix bundle of the two conserved regions (CRs). Two M-subunits and a single S-subunit form an oligomeric protein that functions as a methyltransferase (M2S1 MTase). Here, we present the crystal structure of the intact MTase from Vibrio vulnificus YJ016 in complex with the DNA-mimicking Ocr protein and the S-adenosyl-L-homocysteine (SAH). This MTase includes the M-domain with a helix tail (M-tail helix) and the S1/2-domain of a TRD and a CR α-helix. The Ocr binds to the cleft of the TRD surface and SAH is located in the pocket within the M-domain. The solution- and negative-staining electron microscopy-based reconstructed (M1S1/2)2 structure reveals a symmetric (S1/2)2 assembly using two CR-helices and two M-tail helices as a pivot, which is plausible for recognizing two DNA regions of same sequence. The conformational flexibility of the minimal M1S1/2 MTase dimer indicates a particular state resembling the structure of M2S1 MTases.
Collapse
Affiliation(s)
- Pil-Won Seo
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia; Max Rubner-Institut, Federal Research Institute of Nutrition and Food, 95326 Kulmbach, Germany
| | - Jun-Ha Kim
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Kumoh National Institute of Technology, 61, Daehak-ro, Gumi, Gyeongbuk 39177, Republic of Korea
| | - Seung-A Hwangbo
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jun-Hong Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji-Won Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Thi Yen Ly Huynh
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Basic Medical Research Building, Chonnam National University Medical College, Hwasun, Jeonnam 58128, Republic of Korea
| | - Soo-Jung Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jimin Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Jie-Oh Lee
- Department of Life Sciences and Institute of Membrane Proteins, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Kyeong Sik Jin
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Suk-Youl Park
- Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Jeong-Sun Kim
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea.
| |
Collapse
|
2
|
Wang H, Yang Z, Liu Y. Systematic characterization of
adenosine triphosphate
response to lung cancer epidermal growth factor receptor missense mutations: A molecular insight into “generic” drug resistance mutations. J CHIN CHEM SOC-TAIP 2020. [DOI: 10.1002/jccs.201900435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hui Wang
- Department of Respiratory Medicine Zhucheng People's Hospital Affiliated to Weifang Medical University Zhucheng China
| | - Zengjian Yang
- Department of Respiratory Medicine Zhucheng People's Hospital Affiliated to Weifang Medical University Zhucheng China
| | - Yanliang Liu
- Department of Respiratory Medicine Zhucheng People's Hospital Affiliated to Weifang Medical University Zhucheng China
| |
Collapse
|
3
|
Sinha D, Bialevich V, Shamayeva K, Guzanova A, Sisakova A, Csefalvay E, Reha D, Krejci L, Carey J, Weiserova M, Ettrich R. A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I. J Mol Model 2018; 24:176. [PMID: 29943199 DOI: 10.1007/s00894-018-3722-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 06/15/2018] [Indexed: 11/27/2022]
Abstract
Type I restriction-modification enzymes differ significantly from the type II enzymes commonly used as molecular biology reagents. On hemi-methylated DNAs type I enzymes like the EcoR124I restriction-modification complex act as conventional adenine methylases at their specific target sequences, but unmethylated targets induce them to translocate thousands of base pairs through the stationary enzyme before cleaving distant sites nonspecifically. EcoR124I is a superfamily 2 DEAD-box helicase like eukaryotic double-strand DNA translocase Rad54, with two RecA-like helicase domains and seven characteristic sequence motifs that are implicated in translocation. In Rad54 a so-called extended region adjacent to motif III is involved in ATPase activity. Although the EcoR124I extended region bears sequence and structural similarities with Rad54, it does not influence ATPase or restriction activity as shown in this work, but mutagenesis of the conserved glycine residue of its motif III does alter ATPase and DNA cleavage activity. Through the lens of molecular dynamics, a full model of HsdR of EcoR124I based on available crystal structures allowed interpretation of functional effects of mutants in motif III and its extended region. The results indicate that the conserved glycine residue of motif III has a role in positioning the two helicase domains.
Collapse
Affiliation(s)
- Dhiraj Sinha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic
| | - Vitali Bialevich
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic
| | - Katsiaryna Shamayeva
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic
| | - Alena Guzanova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4, Czech Republic
| | - Alexandra Sisakova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Kamenice 5/A7, 625 00, Brno, Czech Republic
| | - Eva Csefalvay
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic
| | - David Reha
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic.,Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic
| | - Lumir Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Kamenice 5/A7, 625 00, Brno, Czech Republic.,National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic.,International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic.,Chemistry Department, Princeton University, Princeton, NJ, 08544-1009, USA
| | - Marie Weiserova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4, Czech Republic
| | - Rüdiger Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic. .,College of Biomedical Sciences, Larkin University, 18301 North Miami Avenue, Miami, FL, 33169, USA.
| |
Collapse
|
4
|
Bialevich V, Sinha D, Shamayeva K, Guzanova A, Řeha D, Csefalvay E, Carey J, Weiserova M, Ettrich RH. The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation. PeerJ 2017; 5:e2887. [PMID: 28133570 PMCID: PMC5248579 DOI: 10.7717/peerj.2887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/08/2016] [Indexed: 01/20/2023] Open
Abstract
Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification family IC and is composed of three subunit types: HsdS, HsdM, and HsdR. DNA cleavage and ATP-dependent DNA translocation activities are housed in the distinct domains of the endonuclease/motor subunit HsdR. Because the multiple functions are integrated in this large subunit of 1,038 residues, a large number of interdomain contacts might be expected. The crystal structure of EcoR124I HsdR reveals a surprisingly sparse number of contacts between helicase domain 2 and the C-terminal helical domain that is thought to be involved in assembly with HsdM. Only two potential hydrogen-bonding contacts are found in a very small contact region. In the present work, the relevance of these two potential hydrogen-bonding interactions for the multiple activities of EcoR124I is evaluated by analysing mutant enzymes using in vivo and in vitro experiments. Molecular dynamics simulations are employed to provide structural interpretation of the functional data. The results indicate that the helical C-terminal domain is involved in the DNA translocation, cleavage, and ATPase activities of HsdR, and a role in controlling those activities is suggested.
Collapse
Affiliation(s)
- Vitali Bialevich
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Dhiraj Sinha
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Katsiaryna Shamayeva
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
| | - Alena Guzanova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - David Řeha
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Eva Csefalvay
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Chemistry Department, Princeton University, Princeton, NJ, United States
| | - Marie Weiserova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Rüdiger H. Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
- College of Medical Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
| |
Collapse
|
5
|
Csefalvay E, Lapkouski M, Guzanova A, Csefalvay L, Baikova T, Shevelev I, Bialevich V, Shamayeva K, Janscak P, Kuta Smatanova I, Panjikar S, Carey J, Weiserova M, Ettrich R. Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme. PLoS One 2015; 10:e0128700. [PMID: 26039067 PMCID: PMC4454674 DOI: 10.1371/journal.pone.0128700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/29/2015] [Indexed: 11/20/2022] Open
Abstract
Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on motor subunit HsdR. Functional coupling of DNA cleavage and translocation is a hallmark of the Type I restriction systems that is consistent with their proposed role in horizontal gene transfer. DNA cleavage occurs at nonspecific sites distant from the cognate recognition sequence, apparently triggered by stalled translocation. The X-ray crystal structure of the complete HsdR subunit from E. coli plasmid R124 suggested that the triggering mechanism involves interdomain contacts mediated by ATP. In the present work, in vivo and in vitro activity assays and crystal structures of three mutants of EcoR124I HsdR designed to probe this mechanism are reported. The results indicate that interdomain engagement via ATP is indeed responsible for signal transmission between the endonuclease and helicase domains of the motor subunit. A previously identified sequence motif that is shared by the RecB nucleases and some Type I endonucleases is implicated in signaling.
Collapse
Affiliation(s)
- Eva Csefalvay
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Mikalai Lapkouski
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Alena Guzanova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Ladislav Csefalvay
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Tatsiana Baikova
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Igor Shevelev
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Vitali Bialevich
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Katsiaryna Shamayeva
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Pavel Janscak
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Institute of Molecular Cancer Research, University of Zürich, Wintherthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Ivana Kuta Smatanova
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Santosh Panjikar
- Australian Synchrotron, 800 Blackburn Road, Clayton VIC 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, VIC 3800 Australia
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
- Chemistry Department, Princeton University, Princeton, New Jersey 08544–1009, United States of America
| | - Marie Weiserova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Rüdiger Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| |
Collapse
|
6
|
Reha D, Harish B, Sinha D, Kukacka Z, McSally J, Ettrichova O, Novak P, Carey J, Ettrich R. Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein. J Mol Model 2014; 20:2400. [PMID: 25152065 DOI: 10.1007/s00894-014-2400-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2013] [Accepted: 07/23/2014] [Indexed: 10/24/2022]
Abstract
WrbA is a novel multimeric flavodoxin-like protein of unknown function. A recent high-resolution X-ray crystal structure of E. coli WrbA holoprotein revealed a methionine sulfoxide residue with full occupancy in the FMN-binding site, a finding that was confirmed by mass spectrometry. In an effort to evaluate whether methionine sulfoxide may have a role in WrbA function, the present analyses were undertaken using molecular dynamics simulations in combination with further mass spectrometry of the protein. Methionine sulfoxide formation upon reconstitution of purified apoWrbA with oxidized FMN is fast as judged by kinetic mass spectrometry, being complete in ∼5 h and resulting in complete conversion at the active-site methionine with minor extents of conversion at heterogeneous second sites. Analysis of methionine oxidation states during purification of holoWrbA from bacterial cells reveals that methionine is not oxidized prior to reconstitution, indicating that methionine sulfoxide is unlikely to be relevant to the function of WrbA in vivo. Although the simulation results, the first reported for WrbA, led to no hypotheses about the role of methionine sulfoxide that could be tested experimentally, they elucidated the origins of the two major differences between apo- and holoWrbA crystal structures, an alteration of inter-subunit distance and a rotational shift within the tetrameric assembly.
Collapse
Affiliation(s)
- David Reha
- Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, 373 33, Nove Hrady, Czech Republic,
| | | | | | | | | | | | | | | | | |
Collapse
|