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- PDB-7lb6: PDX1.2/PDX1.3 co-expression complex -

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Basic information

Entry
Database: PDB / ID: 7lb6
TitlePDX1.2/PDX1.3 co-expression complex
Components
  • Pyridoxal 5'-phosphate synthase subunit PDX1.3
  • Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
KeywordsPLANT PROTEIN / pseudoenzyme / dodecamer / vitamin B6
Function / homology
Function and homology information


response to non-ionic osmotic stress / response to lipid hydroperoxide / chlorophyll metabolic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / hyperosmotic salinity response / pyridoxal phosphate biosynthetic process / response to UV-B / amino acid metabolic process / endomembrane system ...response to non-ionic osmotic stress / response to lipid hydroperoxide / chlorophyll metabolic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / hyperosmotic salinity response / pyridoxal phosphate biosynthetic process / response to UV-B / amino acid metabolic process / endomembrane system / response to salt stress / response to oxidative stress / protein heterodimerization activity / protein homodimerization activity / plasma membrane / cytosol
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PDX1.3 / Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.16 Å
AuthorsNovikova, I.V. / Evans, J.E.
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)66382 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
CitationJournal: ACS Chem Biol / Year: 2021
Title: Tunable Heteroassembly of a Plant Pseudoenzyme-Enzyme Complex.
Authors: Irina V Novikova / Mowei Zhou / Chen Du / Marcelina Parra / Doo Nam Kim / Zachary L VanAernum / Jared B Shaw / Hanjo Hellmann / Vicki H Wysocki / James E Evans /
Abstract: Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is ...Pseudoenzymes have emerged as key regulatory elements in all kingdoms of life despite being catalytically nonactive. Yet many factors defining why one protein is active while its homologue is inactive remain uncertain. For pseudoenzyme-enzyme pairs, the similarity of both subunits can often hinder conventional characterization approaches. In plants, a pseudoenzyme, PDX1.2, positively regulates vitamin B production by association with its active catalytic homologues such as PDX1.3 through an unknown assembly mechanism. Here we used an integrative experimental approach to learn that such pseudoenzyme-enzyme pair associations result in heterocomplexes of variable stoichiometry, which are unexpectedly tunable. We also present the atomic structure of the PDX1.2 pseudoenzyme as well as the population averaged PDX1.2-PDX1.3 pseudoenzyme-enzyme pair. Finally, we dissected hetero-dodecamers of each stoichiometry to understand the arrangement of monomers in the heterocomplexes and identified symmetry-imposed preferences in PDX1.2-PDX1.3 interactions. Our results provide a new model of pseudoenzyme-enzyme interactions and their native heterogeneity.
History
DepositionJan 7, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: 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

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Assembly

Deposited unit
A: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
B: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
C: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
D: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
E: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
F: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
G: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
H: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
I: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
J: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
K: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
L: Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
M: Pyridoxal 5'-phosphate synthase subunit PDX1.3
N: Pyridoxal 5'-phosphate synthase subunit PDX1.3
O: Pyridoxal 5'-phosphate synthase subunit PDX1.3
P: Pyridoxal 5'-phosphate synthase subunit PDX1.3
Q: Pyridoxal 5'-phosphate synthase subunit PDX1.3
R: Pyridoxal 5'-phosphate synthase subunit PDX1.3
S: Pyridoxal 5'-phosphate synthase subunit PDX1.3
T: Pyridoxal 5'-phosphate synthase subunit PDX1.3
U: Pyridoxal 5'-phosphate synthase subunit PDX1.3
V: Pyridoxal 5'-phosphate synthase subunit PDX1.3
W: Pyridoxal 5'-phosphate synthase subunit PDX1.3
X: Pyridoxal 5'-phosphate synthase subunit PDX1.3


Theoretical massNumber of molelcules
Total (without water)886,60224
Polymers886,60224
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 / AtPDX1 / 3


Mass: 37408.004 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDX12, A37, PDX1L2, At3g16050, MSL1.3 / Production host: Triticum aestivum (bread wheat) / References: UniProt: Q9ZNR6
#2: Protein
Pyridoxal 5'-phosphate synthase subunit PDX1.3 / PLP synthase subunit PDX1.3


Mass: 36475.531 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PDX13, GIP2, PDX1L3, RSR4, At5g01410, T10O8.120 / Production host: Triticum aestivum (bread wheat)
References: UniProt: Q8L940, pyridoxal 5'-phosphate synthase (glutamine hydrolysing)

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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: PDX1.2/PDX1.3 heterododecamer / Type: COMPLEX
Details: Represents an average 3D class for all PDX1.2/PDX1.3 heterododecamers
Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.445 MDa / Experimental value: YES
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Triticum aestivum (bread wheat)
Buffer solutionpH: 7.5 / Details: 50 mM Tris, 150 mM NaCl, 4 mM DTT
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: at 15 mA / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 85 % / Chamber temperature: 298 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 FIELDBright-field microscopy / Cs: 2.7 mm
Image recordingElectron dose: 100 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
1cryoSPARC2.5particle selection
2SerialEMimage acquisition
4cryoSPARC2.5CTF correctionCTFFIND4
9cryoSPARC2.5initial Euler assignment
10cryoSPARC2.5final Euler assignment
11cryoSPARC2.5classification
12cryoSPARC2.53D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 510660
SymmetryPoint symmetry: D6 (2x6 fold dihedral)
3D reconstructionResolution: 3.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 286642 / Symmetry type: POINT

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