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- PDB-8hla: Heteromeric ring comprised of peroxiredoxin from Thermococcus kod... -

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Basic information

Entry
Database: PDB / ID: 8hla
TitleHeteromeric ring comprised of peroxiredoxin from Thermococcus kodakaraensis (TkPrx) F42C/C46S/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F42C) and TkPrx C46S/F76C/C205S/C211S mutant modified with 2-(bromoacetyl)naphthalene (Naph@TkPrx*F76C) (Naph@(MIX|3:3))
Components(Peroxiredoxin) x 2
KeywordsOXIDOREDUCTASE / Peroxiredoxin / Complex / Protein protein interactions
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin activity / thioredoxin-dependent peroxiredoxin / cell redox homeostasis / cytosol
Similarity search - Function
Peroxiredoxin, TDXH subfamily / 1-Cys peroxiredoxin / Peroxiredoxin, AhpC-type / Peroxiredoxin, C-terminal / C-terminal domain of 1-Cys peroxiredoxin / Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant / AhpC/TSA family / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
1-naphthalen-2-ylethanone / Peroxiredoxin
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å
AuthorsHimiyama, T. / Hamaguchi, T. / Yonekura, K. / Nakamura, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)jp22ama121006 Japan
CitationJournal: Bioconjug Chem / Year: 2023
Title: Unnaturally Distorted Hexagonal Protein Ring Alternatingly Reorganized from Two Distinct Chemically Modified Proteins.
Authors: Tomoki Himiyama / Tasuku Hamaguchi / Koji Yonekura / Tsutomu Nakamura /
Abstract: In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein ...In this study, we constructed a semiartificial protein assembly of alternating ring type, which was modified from the natural assembly state via incorporation of a synthetic component at the protein interface. For the redesign of a natural protein assembly, a scrap-and-build approach employing chemical modification was used. Two different protein dimer units were designed based on peroxiredoxin from , which originally forms a dodecameric hexagonal ring with six homodimers. The two dimeric mutants were reorganized into a ring by reconstructing the protein-protein interactions via synthetic naphthalene moieties introduced by chemical modification. Cryo-electron microscopy revealed the formation of a uniquely shaped dodecameric hexagonal protein ring with broken symmetry, distorted from the regular hexagon of the wild-type protein. The artificially installed naphthalene moieties were arranged at the interfaces of dimer units, forming two distinct protein-protein interactions, one of which is highly unnatural. This study deciphered the potential of the chemical modification technique that constructs semiartificial protein structures and assembly hardly accessible by conventional amino acid mutations.
History
DepositionNov 29, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peroxiredoxin
B: Peroxiredoxin
C: Peroxiredoxin
D: Peroxiredoxin
E: Peroxiredoxin
F: Peroxiredoxin
G: Peroxiredoxin
H: Peroxiredoxin
I: Peroxiredoxin
J: Peroxiredoxin
K: Peroxiredoxin
L: Peroxiredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)297,06424
Polymers295,02212
Non-polymers2,04212
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Peroxiredoxin / / Thioredoxin peroxidase / Thioredoxin-dependent peroxiredoxin


Mass: 24585.141 Da / Num. of mol.: 6 / Mutation: C46S,F76C,C205S,C211S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: TK0537 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JF30, thioredoxin-dependent peroxiredoxin
#2: Protein
Peroxiredoxin / / Thioredoxin peroxidase / Thioredoxin-dependent peroxiredoxin


Mass: 24585.143 Da / Num. of mol.: 6 / Mutation: F42C,C46S,C205S,C211S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: TK0537 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5JF30, thioredoxin-dependent peroxiredoxin
#3: Chemical
ChemComp-FL3 / 1-naphthalen-2-ylethanone


Mass: 170.207 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C12H10O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: Naph@MIX / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Thermococcus kodakarensis KOD1 (archaea)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 99 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 60000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: JEOL CRYOSPECPORTER / Temperature (min): 89 K
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)
EM imaging opticsEnergyfilter name: In-column Omega Filter
Image scansWidth: 5760 / Height: 4092

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 599283 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01121420
ELECTRON MICROSCOPYf_angle_d0.93829064
ELECTRON MICROSCOPYf_dihedral_angle_d21.392880
ELECTRON MICROSCOPYf_chiral_restr0.0653144
ELECTRON MICROSCOPYf_plane_restr0.0063684

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