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- EMDB-15953: T3 SAM lyase in complex with S-adenosylmethionine synthase -

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Basic information

Entry
Database: EMDB / ID: EMD-15953
TitleT3 SAM lyase in complex with S-adenosylmethionine synthase
Map data
Sample
  • Complex: T3 SAM lyase in complex with E. coli S-adenosylmethionine synthase.
    • Complex: S-adenosylmethionine synthase in complex with T3 SAM lyase.
      • Protein or peptide: S-adenosylmethionine synthase
      • Protein or peptide: S-Adenosylmethionine lyase
    • Complex: T3 SAM lyase in complex with S-adenosylmethionine synthase.
  • Ligand: CHLORIDE ION
  • Ligand: water
KeywordsSAM lyase / complex / LYASE
Function / homology
Function and homology information


S-adenosyl-L-methionine lyase / S-adenosyl-L-methionine lyase activity / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / S-adenosylmethionine cycle / potassium ion binding / one-carbon metabolic process / transferase activity / magnesium ion binding ...S-adenosyl-L-methionine lyase / S-adenosyl-L-methionine lyase activity / methionine adenosyltransferase / methionine adenosyltransferase activity / S-adenosylmethionine biosynthetic process / S-adenosylmethionine cycle / potassium ion binding / one-carbon metabolic process / transferase activity / magnesium ion binding / ATP binding / identical protein binding / cytosol
Similarity search - Function
S-adenosyl-L-methionine hydrolase / S-Adenosylmethionine lyase family / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain ...S-adenosyl-L-methionine hydrolase / S-Adenosylmethionine lyase family / S-adenosylmethionine synthetase / S-adenosylmethionine synthetase, N-terminal / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal / S-adenosylmethionine synthetase, conserved site / S-adenosylmethionine synthetase superfamily / S-adenosylmethionine synthetase, N-terminal domain / S-adenosylmethionine synthetase, central domain / S-adenosylmethionine synthetase, C-terminal domain / S-adenosylmethionine synthase signature 1. / S-adenosylmethionine synthase signature 2.
Similarity search - Domain/homology
S-Adenosylmethionine lyase / S-adenosylmethionine synthase
Similarity search - Component
Biological speciesEnterobacteria phage T3 (virus) / Escherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsTriguis S / Selmer M
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research Council2017-03827 Sweden
Knut and Alice Wallenberg FoundationEvolution of new genes and proteins Sweden
CitationJournal: Cell Rep / Year: 2023
Title: Phage T3 overcomes the BREX defense through SAM cleavage and inhibition of SAM synthesis by SAM lyase.
Authors: Aleksandr Andriianov / Silvia Trigüis / Alena Drobiazko / Nicolas Sierro / Nikolai V Ivanov / Maria Selmer / Konstantin Severinov / Artem Isaev /
Abstract: Bacteriophage T3 encodes a SAMase that, through cleavage of S-adenosyl methionine (SAM), circumvents the SAM-dependent type I restriction-modification (R-M) defense. We show that SAMase also allows ...Bacteriophage T3 encodes a SAMase that, through cleavage of S-adenosyl methionine (SAM), circumvents the SAM-dependent type I restriction-modification (R-M) defense. We show that SAMase also allows T3 to evade the BREX defense. Although SAM depletion weakly affects BREX methylation, it completely inhibits the defensive function of BREX, suggesting that SAM could be a co-factor for BREX-mediated exclusion of phage DNA, similar to its anti-defense role in type I R-M. The anti-BREX activity of T3 SAMase is mediated not just by enzymatic degradation of SAM but also by direct inhibition of MetK, the host SAM synthase. We present a 2.8 Å cryoelectron microscopy (cryo-EM) structure of the eight-subunit T3 SAMase-MetK complex. Structure-guided mutagenesis reveals that this interaction stabilizes T3 SAMase in vivo, further stimulating its anti-BREX activity. This work provides insights in the versatility of bacteriophage counterdefense mechanisms and highlights the role of SAM as a co-factor of diverse bacterial immunity systems.
History
DepositionOct 12, 2022-
Header (metadata) releaseAug 23, 2023-
Map releaseAug 23, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15953.png

Downloads & links

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Map

FileDownload / File: emd_15953.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 480 pix.
= 534. Å		1.11 Å/pix.
x 480 pix.
= 534. Å		1.11 Å/pix.
x 480 pix.
= 534. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.14
Minimum - Maximum-0.38827905 - 0.8999983
Average (Standard dev.)-0.0002465498 (±0.011427064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 534.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15953_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15953_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15953_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T3 SAM lyase in complex with E. coli S-adenosylmethionine synthase.

EntireName: T3 SAM lyase in complex with E. coli S-adenosylmethionine synthase.
Components
  • Complex: T3 SAM lyase in complex with E. coli S-adenosylmethionine synthase.
    • Complex: S-adenosylmethionine synthase in complex with T3 SAM lyase.
      • Protein or peptide: S-adenosylmethionine synthase
      • Protein or peptide: S-Adenosylmethionine lyase
    • Complex: T3 SAM lyase in complex with S-adenosylmethionine synthase.
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: T3 SAM lyase in complex with E. coli S-adenosylmethionine synthase.

SupramoleculeName: T3 SAM lyase in complex with E. coli S-adenosylmethionine synthase.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: T3 SAM lyase was recombinantly expressed in E. coli Top10 and co-purified in complex with S-adenosylmethionine synthase from the host.
Source (natural)Organism: Enterobacteria phage T3 (virus)
Molecular weightTheoretical: 239 KDa

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Supramolecule #2: S-adenosylmethionine synthase in complex with T3 SAM lyase.

SupramoleculeName: S-adenosylmethionine synthase in complex with T3 SAM lyase.
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Details: T3 SAM lyase was recombinantly expressed in E. coli Top10 and co-purified in complex with S-adenosylmethionine synthase from the host.
Source (natural)Organism: Escherichia coli (E. coli) / Strain: Top10

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Supramolecule #3: T3 SAM lyase in complex with S-adenosylmethionine synthase.

SupramoleculeName: T3 SAM lyase in complex with S-adenosylmethionine synthase.
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Details: T3 SAM lyase was recombinantly expressed in E. coli Top10 and co-purified in complex with S-adenosylmethionine synthase from the host.
Source (natural)Organism: Enterobacteria phage T3 (virus)

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Macromolecule #1: S-adenosylmethionine synthase

MacromoleculeName: S-adenosylmethionine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: methionine adenosyltransferase
Source (natural)Organism: Escherichia coli (E. coli) / Strain: K12
Molecular weightTheoretical: 41.998508 KDa
SequenceString: MAKHLFTSES VSEGHPDKIA DQISDAVLDA ILEQDPKARV ACETYVKTGM VLVGGEITTS AWVDIEEITR NTVREIGYVH SDMGFDANS CAVLSAIGKQ SPDINQGVDR ADPLEQGAGD QGLMFGYATN ETDVLMPAPI TYAHRLVQRQ AEVRKNGTLP W LRPDAKSQ ...String:
MAKHLFTSES VSEGHPDKIA DQISDAVLDA ILEQDPKARV ACETYVKTGM VLVGGEITTS AWVDIEEITR NTVREIGYVH SDMGFDANS CAVLSAIGKQ SPDINQGVDR ADPLEQGAGD QGLMFGYATN ETDVLMPAPI TYAHRLVQRQ AEVRKNGTLP W LRPDAKSQ VTFQYDDGKI VGIDAVVLST QHSEEIDQKS LQEAVMEEII KPILPAEWLT SATKFFINPT GRFVIGGPMG DC GLTGRKI IVDTYGGMAR HGGGAFSGKD PSKVDRSAAY AARYVAKNIV AAGLADRCEI QVSYAIGVAE PTSIMVETFG TEK VPSEQL TLLVREFFDL RPYGLIQMLD LLHPIYKETA AYGHFGREHF PWEKTDKAQL LRDAAGLK

UniProtKB: S-adenosylmethionine synthase

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Macromolecule #2: S-Adenosylmethionine lyase

MacromoleculeName: S-Adenosylmethionine lyase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO / EC number: ec: 2.5.1.4
Source (natural)Organism: Enterobacteria phage T3 (virus)
Molecular weightTheoretical: 17.863264 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MIFTKEPANV FYVLVSAFRS NLCDEVNMSR HRHMVSTLRA APGLYGSVES TDLTGCYREA ISSAPTEEKT VRVRCKDKAQ ALNVARLAC NEWEQDCVLV YKSQTHTAGL VYAKGIDGYK AERLPGSFQE VPKGAPLQGC FTIDEFGRRW QVQHHHHHH

UniProtKB: S-Adenosylmethionine lyase

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Macromolecule #3: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 24 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.125 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
25.0 mMNH2C(CH2OH)3Tris(Hydroxymethyl)aminomethane
150.0 mMNaClSodium chloride
2.5 mMHSCH2CH2OH2-Mercaptoethanol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.039 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting for 3 seconds before plunging..

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 1 / Number real images: 5447 / Average exposure time: 3.0 sec. / Average electron dose: 47.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.1 µm / Calibrated defocus min: 0.35000000000000003 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1445186
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3) / Number images used: 244912
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3)
Details: 3D classification was used to remove particles with incomplete occupancy of T3 SAMase.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

1p7l

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-8bb1:
T3 SAM lyase in complex with S-adenosylmethionine synthase

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