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- PDB-8qzp: Structure of the non-mitochondrial citrate synthase from Ananas c... -

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Basic information

Entry
Database: PDB / ID: 8qzp
TitleStructure of the non-mitochondrial citrate synthase from Ananas comosus
ComponentsCitrate synthase
KeywordsTRANSFERASE / Complex
Function / homology
Function and homology information


citrate (Si)-synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process / mitochondrial matrix
Similarity search - Function
Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase
Similarity search - Domain/homology
Biological speciesAnanas comosus (pineapple)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.15 Å
AuthorsLo, Y.K. / Bohn, S. / Sendker, F.L. / Schuller, J.M. / Hochberg, G.
Funding support Germany, European Union, 3items
OrganizationGrant numberCountry
Max Planck Society Germany
German Research Foundation (DFG)SCHU3364/1-1 Germany
European Research Council (ERC)101040472 EVOCATIONEuropean Union
CitationJournal: bioRxiv / Year: 2024
Title: Frequent transitions in self-assembly across the evolution of a central metabolic enzyme.
Authors: Franziska L Sendker / Tabea Schlotthauer / Christopher-Nils Mais / Yat Kei Lo / Mathias Girbig / Stefan Bohn / Thomas Heimerl / Daniel Schindler / Arielle Weinstein / Brain P Metzger / ...Authors: Franziska L Sendker / Tabea Schlotthauer / Christopher-Nils Mais / Yat Kei Lo / Mathias Girbig / Stefan Bohn / Thomas Heimerl / Daniel Schindler / Arielle Weinstein / Brain P Metzger / Joseph W Thornton / Arvind Pillai / Gert Bange / Jan M Schuller / Georg K A Hochberg /
Abstract: Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are ...Many enzymes assemble into homomeric protein complexes comprising multiple copies of one protein. Because structural form is usually assumed to follow function in biochemistry, these assemblies are thought to evolve because they provide some functional advantage. In many cases, however, no specific advantage is known and, in some cases, quaternary structure varies among orthologs. This has led to the proposition that self-assembly may instead vary neutrally within protein families. The extent of such variation has been difficult to ascertain because quaternary structure has until recently been difficult to measure on large scales. Here, we employ mass photometry, phylogenetics, and structural biology to interrogate the evolution of homo-oligomeric assembly across the entire phylogeny of prokaryotic citrate synthases - an enzyme with a highly conserved function. We discover a menagerie of different assembly types that come and go over the course of evolution, including cases of parallel evolution and reversions from complex to simple assemblies. Functional experiments in vitro and in vivo indicate that evolutionary transitions between different assemblies do not strongly influence enzyme catalysis. Our work suggests that enzymes can wander relatively freely through a large space of possible assemblies and demonstrates the power of characterizing structure-function relationships across entire phylogenies.
History
DepositionOct 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2024Provider: repository / Type: Initial release

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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
G: Citrate synthase
H: Citrate synthase


Theoretical massNumber of molelcules
Total (without water)460,8948
Polymers460,8948
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Citrate synthase


Mass: 57611.801 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ananas comosus (pineapple) / Gene: LOC109710921 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6P5F0R3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Octameric complex of non-mitochondrial/glyoxysomal citrate synthase from Ananas comosus
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Ananas comosus (pineapple)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.3
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 29000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.15 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 108304 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00426122
ELECTRON MICROSCOPYf_angle_d0.73235481
ELECTRON MICROSCOPYf_dihedral_angle_d6.0293664
ELECTRON MICROSCOPYf_chiral_restr0.0433885
ELECTRON MICROSCOPYf_plane_restr0.0064624

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