7LB5

Pyridoxal 5'-phosphate synthase-like subunit PDX1.2 (Arabidopsis thaliana)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Tunable Heteroassembly of a Plant Pseudoenzyme-Enzyme Complex.

Novikova, I.V.Zhou, M.Du, C.Parra, M.Kim, D.N.VanAernum, Z.L.Shaw, J.B.Hellmann, H.Wysocki, V.H.Evans, J.E.

(2021) ACS Chem Biol 16: 2315-2325

  • DOI: https://doi.org/10.1021/acschembio.1c00475
  • Primary Citation of Related Structures:  
    7LB5, 7LB6

  • PubMed 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 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 6 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.


  • Organizational Affiliation

    Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyridoxal 5'-phosphate synthase-like subunit PDX1.2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
348Arabidopsis thalianaMutation(s): 0 
Gene Names: PDX12A37PDX1L2At3g16050MSL1.3
UniProt
Find proteins for Q9ZNR6 (Arabidopsis thaliana)
Explore Q9ZNR6 
Go to UniProtKB:  Q9ZNR6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZNR6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.16 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.5
MODEL REFINEMENTPHENIX1.15-3459

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States66382
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU24GM129547

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-22
    Type: Initial release
  • Version 1.1: 2021-12-01
    Changes: Database references