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TitleEmergence of fractal geometries in the evolution of a metabolic enzyme.
Journal, issue, pagesNature, Vol. 628, Issue 8009, Page 894-900, Year 2024
Publish dateApr 10, 2024
AuthorsFranziska 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 /
PubMed AbstractFractals 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.
External linksNature / PubMed:38600380 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution2.71 - 5.91 Å
Structure data

15529

8an1

EMDB-15529, PDB-8an1:
Structure of a first level Sierpinski triangle formed by a citrate synthase
Method: EM (single particle) / Resolution: 3.93 Å

16004

8bei

EMDB-16004, PDB-8bei:
Structure of hexameric subcomplexes (Truncation Delta2-6) of the fractal citrate synthase from Synechococcus elongatus PCC7942
Method: EM (single particle) / Resolution: 3.06 Å

19250

8rjk

EMDB-19250, PDB-8rjk:
Pseudoatomic model of a second-order Sierpinski triangle formed by the citrate synthase from Synechococcus elongatus
Method: EM (single particle) / Resolution: 5.91 Å

19251

8rjl

EMDB-19251, PDB-8rjl:
Structure of a first order Sierpinski triangle formed by the H369R mutant of the citrate synthase from Synechococcus elongatus
Method: EM (single particle) / Resolution: 3.34 Å

PDB-8bp7:
Citrate-bound hexamer of Synechococcus elongatus citrate synthase
Method: X-RAY DIFFRACTION / Resolution: 2.71 Å

Chemicals

ChemComp-SO4:
SULFATE ION

ChemComp-CIT:
CITRIC ACID

ChemComp-MG:
Unknown entry

ChemComp-HOH:
WATER

Source
  • synechococcus elongatus pcc 7942 = fachb-805 (bacteria)
KeywordsTRANSFERASE / Fractal complex / Krebs-cycle / TCA-cycle / szierpinski triangle

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