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- EMDB-41232: Cryo-EM structure of the Methanosarcina mazei glutamine synthetas... -

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Basic information

Entry
Database: EMDB / ID: EMD-41232
TitleCryo-EM structure of the Methanosarcina mazei glutamine synthetase (GS) with Met-Sox-P and ADP
Map dataMm GS TS map
Sample
  • Complex: M. mazei Glutamine Synthetase (GS) transition state complex
    • Protein or peptide: Glutamine synthetase
  • Ligand: MAGNESIUM ION
  • Ligand: L-METHIONINE-S-SULFOXIMINE PHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordsglutamine synthetase / GS / transition state / MSO / Met-Sox-P / ADP / LIGASE
Function / homology
Function and homology information


glutamine synthetase / glutamine biosynthetic process / glutamine synthetase activity / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Glutamine synthetase type I / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain ...Glutamine synthetase type I / Glutamine synthetase, N-terminal conserved site / Glutamine synthetase signature 1. / Glutamine synthetase, beta-Grasp domain / Glutamine synthetase (GS) beta-grasp domain profile. / Glutamine synthetase, glycine-rich site / Glutamine synthetase putative ATP-binding region signature. / Glutamine synthetase, N-terminal domain superfamily / Glutamine synthetase (GS) catalytic domain profile. / Glutamine synthetase, catalytic domain / Glutamine synthetase, N-terminal domain / Glutamine synthetase, catalytic domain / Glutamine synthetase, catalytic domain / Glutamine synthetase/guanido kinase, catalytic domain
Similarity search - Domain/homology
Glutamine synthetase
Similarity search - Component
Biological speciesMethanosarcina mazei Go1 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.66 Å
AuthorsSchumacher MA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM130290 United States
CitationJournal: Nat Commun / Year: 2023
Title: M. mazei glutamine synthetase and glutamine synthetase-GlnK1 structures reveal enzyme regulation by oligomer modulation.
Authors: Maria A Schumacher / Raul Salinas / Brady A Travis / Rajiv Ranjan Singh / Nicholas Lent /
Abstract: Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi- ...Glutamine synthetases (GS) play central roles in cellular nitrogen assimilation. Although GS active-site formation requires the oligomerization of just two GS subunits, all GS form large, multi-oligomeric machines. Here we describe a structural dissection of the archaeal Methanosarcina mazei (Mm) GS and its regulation. We show that Mm GS forms unstable dodecamers. Strikingly, we show this Mm GS oligomerization property is leveraged for a unique mode of regulation whereby labile Mm GS hexamers are stabilized by binding the nitrogen regulatory protein, GlnK1. Our GS-GlnK1 structure shows that GlnK1 functions as molecular glue to affix GS hexamers together, stabilizing formation of GS active-sites. These data, therefore, reveal the structural basis for a unique form of enzyme regulation by oligomer modulation.
History
DepositionJul 11, 2023-
Header (metadata) releaseNov 15, 2023-
Map releaseNov 15, 2023-
UpdateNov 29, 2023-
Current statusNov 29, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41232.png

Downloads & links

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Map

FileDownload / File: emd_41232.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMm GS TS map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.88 Å/pix.
x 280 pix.
= 246.4 Å		0.88 Å/pix.
x 280 pix.
= 246.4 Å		0.88 Å/pix.
x 280 pix.
= 246.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.88 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.332
Minimum - Maximum-1.1248556 - 1.6480627
Average (Standard dev.)0.001777879 (±0.07980678)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 246.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Mm GS TS half map A

Fileemd_41232_half_map_1.map
AnnotationMm GS TS half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Mm GS TS half map B

Fileemd_41232_half_map_2.map
AnnotationMm GS TS half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : M. mazei Glutamine Synthetase (GS) transition state complex

EntireName: M. mazei Glutamine Synthetase (GS) transition state complex
Components
  • Complex: M. mazei Glutamine Synthetase (GS) transition state complex
    • Protein or peptide: Glutamine synthetase
  • Ligand: MAGNESIUM ION
  • Ligand: L-METHIONINE-S-SULFOXIMINE PHOSPHATE
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: M. mazei Glutamine Synthetase (GS) transition state complex

SupramoleculeName: M. mazei Glutamine Synthetase (GS) transition state complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)

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Macromolecule #1: Glutamine synthetase

MacromoleculeName: Glutamine synthetase / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO / EC number: glutamine synthetase
Source (natural)Organism: Methanosarcina mazei Go1 (archaea)
Molecular weightTheoretical: 52.827926 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MVQMKKCTTK EDVLEAVKER DVKFIRTQFT DTLGIIKSWA IPAEQLEEAF ENGVMFDGSS IQGFTRIEE SDMKLALDPS TFRILPWRPA TGAVARILGD VYLPDGNPFK GDPRYVLKTA IKEAEKMGFS MNVGPELEFF L FKLDANGN ...String:
MGSSHHHHHH SSGLVPRGSH MVQMKKCTTK EDVLEAVKER DVKFIRTQFT DTLGIIKSWA IPAEQLEEAF ENGVMFDGSS IQGFTRIEE SDMKLALDPS TFRILPWRPA TGAVARILGD VYLPDGNPFK GDPRYVLKTA IKEAEKMGFS MNVGPELEFF L FKLDANGN PTTELTDQGG YFDFAPLDRA QDVRRDIDYA LEHMGFQIEA SHHEVAPSQH EIDFRFGDVL CTADNVVTFK YV VKSIAYH KGYYASFMPK PLFGVNGSGM HSNQSLFKDG KNVFYDPDTP TKLSQDAMYY IGGLLKHIRE FTAVTNPVVN SYK RLVPGY EAPVYISWSA QNRSSLIRIP ATRGNGTRIE LRCPDPACNP YLAFALMLRA GLEGIKNKID PGEPTNVNIF HLSD KEREE RGIRSLPADL KEAIDEMKGS KFVKEALGEH VFSHYLCAKE MEWDEYKAVV HPWELSRYLS ML

UniProtKB: Glutamine synthetase

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 36 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: L-METHIONINE-S-SULFOXIMINE PHOSPHATE

MacromoleculeName: L-METHIONINE-S-SULFOXIMINE PHOSPHATE / type: ligand / ID: 3 / Number of copies: 12 / Formula: P3S
Molecular weightTheoretical: 260.205 Da
Chemical component information

ChemComp-P3S:
L-METHIONINE-S-SULFOXIMINE PHOSPHATE

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Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 12 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7tdp

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 164400
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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