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- PDB-8bp7: Citrate-bound hexamer of Synechococcus elongatus citrate synthase -

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Basic information

Entry
Database: PDB / ID: 8bp7
TitleCitrate-bound hexamer of Synechococcus elongatus citrate synthase
ComponentsCitrate synthase
KeywordsTRANSFERASE / Krebs-cycle / TCA-cycle / szierpinski triangle
Function / homology
Function and homology information


citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / cytosol
Similarity search - Function
2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain
Similarity search - Domain/homology
CITRIC ACID / Citrate synthase
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsMais, C.-N. / Sendker, F. / Bange, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nature / Year: 2024
Title: Emergence of fractal geometries in the evolution of a metabolic enzyme.
Authors: Franziska L Sendker / Yat Kei Lo / Thomas Heimerl / Stefan Bohn / Louise J Persson / Christopher-Nils Mais / Wiktoria Sadowska / Nicole Paczia / Eva Nußbaum / María Del Carmen Sánchez ...Authors: Franziska L Sendker / Yat Kei Lo / Thomas Heimerl / Stefan Bohn / Louise J Persson / Christopher-Nils Mais / Wiktoria Sadowska / Nicole Paczia / Eva Nußbaum / María Del Carmen Sánchez Olmos / Karl Forchhammer / Daniel Schindler / Tobias J Erb / Justin L P Benesch / Erik G Marklund / Gert Bange / Jan M Schuller / Georg K A Hochberg /
Abstract: Fractals are patterns that are self-similar across multiple length-scales. Macroscopic fractals are common in nature; however, so far, molecular assembly into fractals is restricted to synthetic ...Fractals are patterns that are self-similar across multiple length-scales. Macroscopic fractals are common in nature; however, so far, molecular assembly into fractals is restricted to synthetic systems. Here we report the discovery of a natural protein, citrate synthase from the cyanobacterium Synechococcus elongatus, which self-assembles into Sierpiński triangles. Using cryo-electron microscopy, we reveal how the fractal assembles from a hexameric building block. Although different stimuli modulate the formation of fractal complexes and these complexes can regulate the enzymatic activity of citrate synthase in vitro, the fractal may not serve a physiological function in vivo. We use ancestral sequence reconstruction to retrace how the citrate synthase fractal evolved from non-fractal precursors, and the results suggest it may have emerged as a harmless evolutionary accident. Our findings expand the space of possible protein complexes and demonstrate that intricate and regulatable assemblies can evolve in a single substitution.
History
DepositionNov 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Citrate synthase
B: Citrate synthase
C: Citrate synthase
D: Citrate synthase
E: Citrate synthase
F: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,01530
Polymers266,2046
Non-polymers2,81124
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, electron microscopy, gel filtration, assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37360 Å2
ΔGint-326 kcal/mol
Surface area84530 Å2
Unit cell
Length a, b, c (Å)170.460, 170.460, 545.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein
Citrate synthase


Mass: 44367.371 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 = FACHB-805 (bacteria)
Gene: Synpcc7942_0612 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q31QM5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.3 Å3/Da / Density % sol: 71.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1 M citrate pH 5.5, 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.97626 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 14, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.71→49.39 Å / Num. obs: 127720 / % possible obs: 99.9 % / Redundancy: 28.6 % / CC1/2: 0.998 / Net I/σ(I): 9.19
Reflection shellResolution: 2.71→2.807 Å / Mean I/σ(I) obs: 0.68 / Num. unique obs: 12503 / CC1/2: 0.25

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8BEI

8bei


Resolution: 2.71→49.39 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2802 6385 5 %
Rwork0.229 --
obs0.2315 127720 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.71→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17571 0 172 149 17892
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00918381
X-RAY DIFFRACTIONf_angle_d1.21425010
X-RAY DIFFRACTIONf_dihedral_angle_d27.8372636
X-RAY DIFFRACTIONf_chiral_restr0.062765
X-RAY DIFFRACTIONf_plane_restr0.0083261
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.71-2.740.42022000.38823791X-RAY DIFFRACTION96
2.74-2.770.45612090.3943982X-RAY DIFFRACTION100
2.77-2.80.3972100.36833987X-RAY DIFFRACTION100
2.8-2.840.40652110.36243997X-RAY DIFFRACTION100
2.84-2.880.41012080.34493957X-RAY DIFFRACTION100
2.88-2.920.37552100.32713991X-RAY DIFFRACTION100
2.92-2.960.39572110.32164007X-RAY DIFFRACTION100
2.96-30.36632090.32373970X-RAY DIFFRACTION100
3-3.050.40452130.30224037X-RAY DIFFRACTION100
3.05-3.10.32542100.26853995X-RAY DIFFRACTION100
3.1-3.150.30952100.27243993X-RAY DIFFRACTION100
3.15-3.210.3482120.28414014X-RAY DIFFRACTION100
3.21-3.270.36222100.28194004X-RAY DIFFRACTION100
3.27-3.340.36262120.294023X-RAY DIFFRACTION100
3.34-3.410.33562120.27064020X-RAY DIFFRACTION100
3.41-3.490.29282100.22983996X-RAY DIFFRACTION100
3.49-3.580.27252120.21884027X-RAY DIFFRACTION100
3.58-3.670.25752120.2164010X-RAY DIFFRACTION100
3.67-3.780.25982130.21334059X-RAY DIFFRACTION100
3.78-3.90.26252120.21224025X-RAY DIFFRACTION100
3.9-4.040.2522140.2054054X-RAY DIFFRACTION100
4.04-4.20.24692130.19944034X-RAY DIFFRACTION100
4.2-4.40.21622140.1824087X-RAY DIFFRACTION100
4.4-4.630.23192130.18314068X-RAY DIFFRACTION100
4.63-4.920.24392160.18884088X-RAY DIFFRACTION100
4.92-5.30.27792170.20024114X-RAY DIFFRACTION100
5.3-5.830.23792170.21414134X-RAY DIFFRACTION100
5.83-6.670.27452190.23424165X-RAY DIFFRACTION100
6.67-8.40.24712230.214239X-RAY DIFFRACTION100
8.4-49.390.24512330.19594467X-RAY DIFFRACTION99

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