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Yorodumi- EMDB-60037: Cryo-EM structure of the E. coli BrxX methyltransferase complexed... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-60037 | |||||||||
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Title | Cryo-EM structure of the E. coli BrxX methyltransferase complexed with Ocr | |||||||||
Map data | ||||||||||
Sample |
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Keywords | methyltransferase / complex / TRANSFERASE | |||||||||
Function / homology | Function and homology information symbiont-mediated evasion of host restriction-modification system / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / DNA modification / methylation / nucleic acid binding / symbiont-mediated suppression of host innate immune response / : Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia phage T7 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.15 Å | |||||||||
Authors | Zhu L / Xu TH / Sun LT | |||||||||
Funding support | China, 2 items
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Citation | Journal: Nucleic Acids Res / Year: 2024 Title: Ocr-mediated suppression of BrxX unveils a phage counter-defense mechanism. Authors: Shen Li / Tianhao Xu / Xinru Meng / Yujuan Yan / Ying Zhou / Lei Duan / Yulong Tang / Li Zhu / Litao Sun / Abstract: The burgeoning crisis of antibiotic resistance has directed attention to bacteriophages as natural antibacterial agents capable of circumventing bacterial defenses. Central to this are the bacterial ...The burgeoning crisis of antibiotic resistance has directed attention to bacteriophages as natural antibacterial agents capable of circumventing bacterial defenses. Central to this are the bacterial defense mechanisms, such as the BREX system, which utilizes the methyltransferase BrxX to protect against phage infection. This study presents the first in vitro characterization of BrxX from Escherichia coli, revealing its substrate-specific recognition and catalytic activity. We demonstrate that BrxX exhibits nonspecific DNA binding but selectively methylates adenine within specific motifs. Kinetic analysis indicates a potential regulation of BrxX by the concentration of its co-substrate, S-adenosylmethionine, and suggests a role for other BREX components in modulating BrxX activity. Furthermore, we elucidate the molecular mechanism by which the T7 phage protein Ocr (Overcoming classical restriction) inhibits BrxX. Despite low sequence homology between BrxX from different bacterial species, Ocr effectively suppresses BrxX's enzymatic activity through high-affinity binding. Cryo-electron microscopy and biophysical analyses reveal that Ocr, a DNA mimic, forms a stable complex with BrxX, highlighting a conserved interaction interface across diverse BrxX variants. Our findings provide insights into the strategic counteraction by phages against bacterial defense systems and offer a foundational understanding of the complex interplay between phages and their bacterial hosts, with implications for the development of phage therapy to combat antibiotic resistance. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_60037.map.gz | 210.9 MB | EMDB map data format | |
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Header (meta data) | emd-60037-v30.xml emd-60037.xml | 15.8 KB 15.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_60037_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_60037.png | 87.6 KB | ||
Filedesc metadata | emd-60037.cif.gz | 6.1 KB | ||
Others | emd_60037_half_map_1.map.gz emd_60037_half_map_2.map.gz | 391.4 MB 391.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-60037 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-60037 | HTTPS FTP |
-Validation report
Summary document | emd_60037_validation.pdf.gz | 815.9 KB | Display | EMDB validaton report |
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Full document | emd_60037_full_validation.pdf.gz | 815.5 KB | Display | |
Data in XML | emd_60037_validation.xml.gz | 25.2 KB | Display | |
Data in CIF | emd_60037_validation.cif.gz | 33 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60037 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-60037 | HTTPS FTP |
-Related structure data
Related structure data | 8zekMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_60037.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_60037_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_60037_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The complex of E. coli BrxX methyltransferase with Ocr from bacte...
Entire | Name: The complex of E. coli BrxX methyltransferase with Ocr from bacteriophage T7 |
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Components |
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-Supramolecule #1: The complex of E. coli BrxX methyltransferase with Ocr from bacte...
Supramolecule | Name: The complex of E. coli BrxX methyltransferase with Ocr from bacteriophage T7 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: site-specific DNA-methyltransferase (adenine-specific)
Macromolecule | Name: site-specific DNA-methyltransferase (adenine-specific) type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: site-specific DNA-methyltransferase (adenine-specific) |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 138.043219 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MNTNNIKKYA PQARNDFRDA VIQKLTTLGI AADKKGNLQI AEAETIGETV RYGQFDYPLS TLPRRERLVK RAREQGFEVL VEHCAYTWF NRLCAIRYME LHGYLDHGFR MLSHPETPTA FEVLDHVPEV AEALLPESKA QLVEMKLSGN QDEALYRELL L GQCHALHH ...String: MNTNNIKKYA PQARNDFRDA VIQKLTTLGI AADKKGNLQI AEAETIGETV RYGQFDYPLS TLPRRERLVK RAREQGFEVL VEHCAYTWF NRLCAIRYME LHGYLDHGFR MLSHPETPTA FEVLDHVPEV AEALLPESKA QLVEMKLSGN QDEALYRELL L GQCHALHH AMPFLFEAVD DEAELLLPDN LTRTDSILRG LVDDIPEEDW EQVEVIGWLY QFYISEKKDA VIGKVVKSED IP AATQLFT PNWIVQYLVQ NSVGRQWLQT YPDSPLKDKM EYYIEPAEQT PEVQAQLAAI TPASIEPESI KVLDPACGSG HIL TEAYNV LKAIYEERGY RTRDIPQLIL ENNIFGLDID DRAAQLSGFA MLMLARQDDR RILGRGVRLN IVSLQESKLD IAEV WTKLN FHQHMQRGSM GDMFTQGTAL ANTDSAEYKL LMRTLALFTS AKTLGSLIQV PQEDEAALKA FLEGLYRLAV EGDIQ QKEA AAELIPYIQQ AWILAQRYDA VVANPPYMGG KGMNGDLKEF AKKQFPDSKS DLFAMFMQHA FSLLKENGFN AQVNMQ SWM FLSSYEALRG WLLDNKTFIT MAHLGARAFG QISGEVVQTT AWVIKNNHSG FYKPVFFRLV DDNEEHKKNN LLNRMNC FK NTLQNDFKKI PGSPIAYWAT LAFINSFLKL PALGTRAVKG LDTNGSIDVF LRRWPEVSIN SFDALGKGNS KWFPIAKG G ELRKWFGNHE YIINYENDGI ELRKNKANLR NKDMYFQEGG TWTVVSTTGF SMRYMPKGFL FDQGGSAVFC ENNDELSIY NILACMNSKY INYSASLICP TLNFTTGDVR KFPVIKNNHL EDLAKKAIEI SKADWNQFET SWEFSKNKLI EHKGNVAYSY ASYCNFQDK LYEQLVNIEK NINNIIEEIL GFKIETTENS ELITLNSNKI YRYGQSETND TFLNRHRSDT ISELISYSVG C QMGRYSLD REGLVYAHEG NKGFADLVAE GAYKTFPADS DGILPLMDDE WFEDDVTSRV KEFVRTVWGE EHLQENLEFI AE SLCLYAI KPKKGESALE TIRRYLSTQF WKDHMKMYKK RPIYWLFSSG KEKAFECLVY LHRYNDATLS RMRTEYVVPL LAR YQANID RLNDQLDEAS GGEATRLKRE RDSLIKKFSE LRSYDDRLRH YADMRISIDL DDGVKVNYGK FGDLLADVKA ITGN APEVI UniProtKB: site-specific DNA-methyltransferase (adenine-specific) |
-Macromolecule #2: Protein Ocr
Macromolecule | Name: Protein Ocr / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia phage T7 (virus) |
Molecular weight | Theoretical: 13.819015 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MAMSNMTYNN VFDHAYEMLK ENIRYDDIRD TDDLHDAIHM AADNAVPHYY ADIFSVMASE GIDLEFEDSG LMPDTKDVIR ILQARIYEQ LTIDLWEDAE DLLNEYLEEV EEYEEDEE UniProtKB: Protein Ocr |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT |
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Output model | PDB-8zek: |