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- EMDB-12809: MAT in complex with SAMH -

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Basic information

Entry
Database: EMDB / ID: EMD-12809
TitleMAT in complex with SAMH
Map dataS-adenosylmethionine hydrolase (SAMH) in complex with methionine S-adenosyltransferase(MAT)
Sample
  • Complex: filaments of METK in complex with SAM hydrolase
    • Complex: S-adenosylmethionine synthase
      • Protein or peptide: S-adenosylmethionine synthase
    • Complex: SAM hydrolase
      • Protein or peptide: SAM hydrolase
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 / one-carbon metabolic process / lyase activity / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
S-adenosyl-L-methionine hydrolase / 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-adenosyl-L-methionine hydrolase / 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 synthase / S-Adenosylmethionine lyase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria) / Escherichia virus T3 / Escherichia coli (strain K12) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsSimon H / Kleiner D / Shmulevich F / Zarivach R / Zalk R / Tang H / Ding F / Bershtein S
Funding support Israel, 1 items
OrganizationGrant numberCountry
Israel Science Foundation1630/15 Israel
CitationJournal: mBio / Year: 2021
Title: SAMase of Bacteriophage T3 Inactivates Escherichia coli's Methionine -Adenosyltransferase by Forming Heteropolymers.
Authors: Hadas Simon-Baram / Daniel Kleiner / Fannia Shmulevich / Raz Zarivach / Ran Zalk / Huayuan Tang / Feng Ding / Shimon Bershtein /
Abstract: -Adenosylmethionine lyase (SAMase) of bacteriophage T3 degrades the intracellular SAM pools of the host Escherichia coli cells, thereby inactivating a crucial metabolite involved in a plethora of ...-Adenosylmethionine lyase (SAMase) of bacteriophage T3 degrades the intracellular SAM pools of the host Escherichia coli cells, thereby inactivating a crucial metabolite involved in a plethora of cellular functions, including DNA methylation. SAMase is the first viral protein expressed upon infection, and its activity prevents methylation of the T3 genome. Maintenance of the phage genome in a fully unmethylated state has a profound effect on the infection strategy. It allows T3 to shift from a lytic infection under normal growth conditions to a transient lysogenic infection under glucose starvation. Using single-particle cryoelectron microscopy (cryo-EM) and biochemical assays, we demonstrate that SAMase performs its function by not only degrading SAM but also by interacting with and efficiently inhibiting the host's methionine -adenosyltransferase (MAT), the enzyme that produces SAM. Specifically, SAMase triggers open-ended head-to-tail assembly of E. coli MAT into an unusual linear filamentous structure in which adjacent MAT tetramers are joined by two SAMase dimers. Molecular dynamics simulations together with normal mode analyses suggest that the entrapment of MAT tetramers within filaments leads to an allosteric inhibition of MAT activity due to a shift to low-frequency, high-amplitude active-site-deforming modes. The amplification of uncorrelated motions between active-site residues weakens MAT's substrate binding affinity, providing a possible explanation for the observed loss of function. We propose that the dual function of SAMase as an enzyme that degrades SAM and as an inhibitor of MAT activity has emerged to achieve an efficient depletion of the intracellular SAM pools. Self-assembly of enzymes into filamentous structures in response to specific metabolic cues has recently emerged as a widespread strategy of metabolic regulation. In many instances, filamentation of metabolic enzymes occurs in response to starvation and leads to functional inactivation. Here, we report that bacteriophage T3 modulates the metabolism of the host E. coli cells by recruiting a similar strategy: silencing a central metabolic enzyme by subjecting it to phage-mediated polymerization. This observation points to an intriguing possibility that virus-induced polymerization of the host metabolic enzymes is a common mechanism implemented by viruses to metabolically reprogram and subdue infected cells.
History
DepositionApr 27, 2021-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateOct 13, 2021-
Current statusOct 13, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ock
  • Surface level: 0.25
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12809.png

Downloads & links

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Map

FileDownload / File: emd_12809.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS-adenosylmethionine hydrolase (SAMH) in complex with methionine S-adenosyltransferase(MAT)
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.12 / Movie #1: 0.25
Minimum - Maximum-0.37523338 - 0.89323926
Average (Standard dev.)0.0014410599 (±0.04181811)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z330.000330.000330.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.3750.8930.001

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Supplemental data

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Sample components

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Entire : filaments of METK in complex with SAM hydrolase

EntireName: filaments of METK in complex with SAM hydrolase
Components
  • Complex: filaments of METK in complex with SAM hydrolase
    • Complex: S-adenosylmethionine synthase
      • Protein or peptide: S-adenosylmethionine synthase
    • Complex: SAM hydrolase
      • Protein or peptide: SAM hydrolase

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Supramolecule #1: filaments of METK in complex with SAM hydrolase

SupramoleculeName: filaments of METK in complex with SAM hydrolase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: S-adenosylmethionine synthase

SupramoleculeName: S-adenosylmethionine synthase / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Escherichia coli K-12 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)

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Supramolecule #3: SAM hydrolase

SupramoleculeName: SAM hydrolase / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Escherichia virus T3
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: S-adenosylmethionine synthase

MacromoleculeName: S-adenosylmethionine synthase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: methionine adenosyltransferase
Source (natural)Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12
Molecular weightTheoretical: 42.827375 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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 LRDAAGLKHH HHHH

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Macromolecule #2: SAM hydrolase

MacromoleculeName: SAM hydrolase / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Escherichia virus T3
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

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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

BufferpH: 8 / Details: 25mM Tris pH 8.0, 150 mM KCl,1 mM DTT.
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 65950
Initial angle assignmentType: OTHER / Details: stochastic gradient descent
Final angle assignmentType: MAXIMUM LIKELIHOOD

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