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- PDB-7ns5: Structure of yeast Fbp1 (Fructose-1,6-bisphosphatase 1) -

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Basic information

Entry
Database: PDB / ID: 7ns5
TitleStructure of yeast Fbp1 (Fructose-1,6-bisphosphatase 1)
ComponentsFructose-1,6-bisphosphataseFructose 1,6-bisphosphatase
KeywordsHYDROLASE / GID / CTLH / ubiquitin / E3 ligase / supramolecular assembly / metabolism / gluconeogenesis / cryoEM
Function / homology
Function and homology information


Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / fructose metabolic process / reactive oxygen species metabolic process / gluconeogenesis / periplasmic space ...Gluconeogenesis / sucrose biosynthetic process / fructose-bisphosphatase / fructose 1,6-bisphosphate 1-phosphatase activity / fructose 1,6-bisphosphate metabolic process / fructose 6-phosphate metabolic process / fructose metabolic process / reactive oxygen species metabolic process / gluconeogenesis / periplasmic space / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Fructose-1,6-bisphosphatase / Fructose-1,6-bisphosphatase, active site / Fructose-1-6-bisphosphatase class 1, C-terminal / Fructose-1-6-bisphosphatase active site. / Fructose-1,6-bisphosphatase class 1 / Fructose-1-6-bisphosphatase class I, N-terminal / Fructose-1-6-bisphosphatase, N-terminal domain / Fructose-1-6-bisphosphatase, C-terminal domain
Similarity search - Domain/homology
PHOSPHATE ION / Fructose-1,6-bisphosphatase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsSherpa, D. / Chrustowicz, J. / Prabu, J.R. / Schulman, B.A.
Funding support Germany, 2items
OrganizationGrant numberCountry
European Research Council (ERC)789016-NEDD8Activate Germany
German Research Foundation (DFG)SCHU 3196/1-1 Germany
Citation
Journal: Mol Cell / Year: 2021
Title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme.
Authors: Dawafuti Sherpa / Jakub Chrustowicz / Shuai Qiao / Christine R Langlois / Laura A Hehl / Karthik Varma Gottemukkala / Fynn M Hansen / Ozge Karayel / Susanne von Gronau / J Rajan Prabu / ...Authors: Dawafuti Sherpa / Jakub Chrustowicz / Shuai Qiao / Christine R Langlois / Laura A Hehl / Karthik Varma Gottemukkala / Fynn M Hansen / Ozge Karayel / Susanne von Gronau / J Rajan Prabu / Matthias Mann / Arno F Alpi / Brenda A Schulman /
Abstract: How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of ...How are E3 ubiquitin ligases configured to match substrate quaternary structures? Here, by studying the yeast GID complex (mutation of which causes deficiency in glucose-induced degradation of gluconeogenic enzymes), we discover supramolecular chelate assembly as an E3 ligase strategy for targeting an oligomeric substrate. Cryoelectron microscopy (cryo-EM) structures show that, to bind the tetrameric substrate fructose-1,6-bisphosphatase (Fbp1), two minimally functional GID E3s assemble into the 20-protein Chelator-GID, which resembles an organometallic supramolecular chelate. The Chelator-GID assembly avidly binds multiple Fbp1 degrons so that multiple Fbp1 protomers are simultaneously ubiquitylated at lysines near the allosteric and substrate binding sites. Importantly, key structural and biochemical features, including capacity for supramolecular assembly, are preserved in the human ortholog, the CTLH E3. Based on our integrative structural, biochemical, and cell biological data, we propose that higher-order E3 ligase assembly generally enables multipronged targeting, capable of simultaneously incapacitating multiple protomers and functionalities of oligomeric substrates.
#1: Journal: Biorxiv / Year: 2021
Title: GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme
Authors: Sherpa, D. / Chrustowicz, J. / Qiao, S. / Langlois, C.R. / Hehl, L.A. / Gottemukkala, K.V. / Hansen, F.M. / Karayel, O. / Prabu, J.R. / Mann, M. / Alpi, A.F. / Schulman, B.A.
History
DepositionMar 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphatase
D: Fructose-1,6-bisphosphatase
B: Fructose-1,6-bisphosphatase
C: Fructose-1,6-bisphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,10416
Polymers156,5294
Non-polymers57412
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17050 Å2
ΔGint-189 kcal/mol
Surface area39720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.018, 133.794, 171.490
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Fructose-1,6-bisphosphatase / Fructose 1,6-bisphosphatase / FBPase / D-fructose-1 / 6-bisphosphate 1-phosphohydrolase


Mass: 39132.340 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: FBP1, YLR377C, L8039.18 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P09201, fructose-bisphosphatase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 277 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 16% PEG 3350, 0.2 M MgCl2 and 0.1 M Bis-Tris pH 6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.946→45.224 Å / Num. obs: 98528 / % possible obs: 99.7 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.04 / Net I/σ(I): 19.73
Reflection shellResolution: 1.95→2.016 Å / Num. unique obs: 15496 / CC1/2: 0.34

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FTA

1fta


Resolution: 1.95→45.22 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 26.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2424 5633 6.24 %
Rwork0.2081 84666 -
obs0.2103 90299 91.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.46 Å2 / Biso mean: 47.4637 Å2 / Biso min: 23.26 Å2
Refinement stepCycle: final / Resolution: 1.95→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9417 0 28 277 9722
Biso mean--53.89 43.85 -
Num. residues----1214
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.970.431400.39371977211766
1.97-1.990.34471490.35622262241174
1.99-2.020.35761560.32232302245876
2.02-2.040.31721570.32092332248978
2.04-2.070.34761730.30262503267681
2.07-2.10.31441650.28332479264482
2.1-2.130.32791620.26012598276084
2.13-2.160.32321710.25442657282886
2.16-2.190.30241780.23962661283988
2.19-2.230.28351820.24412784296690
2.23-2.270.2991800.23152723290389
2.27-2.310.26891880.21952812300092
2.31-2.350.24581790.20742835301492
2.35-2.40.26111920.20782845303793
2.4-2.450.25421900.2152878306894
2.45-2.510.23991940.21892894308894
2.51-2.570.24261910.21412917310895
2.57-2.640.25381990.21322989318897
2.64-2.720.27072010.20942971317297
2.72-2.810.27932080.2073015322398
2.81-2.910.22742000.21073044324498
2.91-3.020.22751980.20883030322899
3.02-3.160.23842100.20563070328099
3.16-3.330.23642020.23080328299
3.33-3.530.24331990.19673085328499
3.54-3.810.21212150.188631263341100
3.81-4.190.19592080.177931343342100
4.19-4.80.18892100.164331493359100
4.8-6.040.22342130.191531833396100
6.04-45.220.25862230.22043331355499
Refinement TLS params.Method: refined / Origin x: 28.7736 Å / Origin y: 4.7597 Å / Origin z: -15.5522 Å
111213212223313233
T0.2463 Å20.0077 Å20.0288 Å2-0.2288 Å2-0.0169 Å2--0.2987 Å2
L1.1459 °2-0.0458 °2-1.0032 °2-0.2247 °20.0647 °2--1.7071 °2
S-0.211 Å °0.0052 Å °-0.1912 Å °-0.0193 Å °0.0161 Å °0.008 Å °0.2579 Å °0.061 Å °0.0817 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA19 - 348
2X-RAY DIFFRACTION1allA350 - 351
3X-RAY DIFFRACTION1allD19 - 345
4X-RAY DIFFRACTION1allD350 - 351
5X-RAY DIFFRACTION1allB20 - 345
6X-RAY DIFFRACTION1allB350 - 351
7X-RAY DIFFRACTION1allC20 - 344
8X-RAY DIFFRACTION1allC350 - 351
9X-RAY DIFFRACTION1allS1 - 428
10X-RAY DIFFRACTION1allE1 - 4

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