8EW9 | pdb_00008ew9

Crystal structure of Saccharomyces cerevisiae Altered Inheritance rate of Mitochondria protein 46 (AIM46p)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.234 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 
    0.174 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Aim18p and Aim46p are chalcone isomerase domain-containing mitochondrial hemoproteins in Saccharomyces cerevisiae.

Schmitz, J.M.Wolters, J.F.Murray, N.H.Guerra, R.M.Bingman, C.A.Hittinger, C.T.Pagliarini, D.J.

(2023) J Biological Chem 299: 102981-102981

  • DOI: https://doi.org/10.1016/j.jbc.2023.102981
  • Primary Citation Related Structures: 
    8EW8, 8EW9

  • PubMed Abstract: 

    Chalcone isomerases (CHIs) have well-established roles in the biosynthesis of plant flavonoid metabolites. Saccharomyces cerevisiae possesses two predicted CHI-like proteins, Aim18p (encoded by YHR198C) and Aim46p (YHR199C), but it lacks other enzymes of the flavonoid pathway, suggesting that Aim18p and Aim46p employ the CHI fold for distinct purposes. Here, we demonstrate using proteinase K protection assays, sodium carbonate extractions, and crystallography that Aim18p and Aim46p reside on the mitochondrial inner membrane and adopt CHI folds, but they lack select active site residues and possess an extra fungal-specific loop. Consistent with these differences, Aim18p and Aim46p lack CHI activity and also the fatty acid-binding capabilities of other CHI-like proteins, but instead bind heme. We further show that diverse fungal homologs also bind heme and that Aim18p and Aim46p possess structural homology to a bacterial hemoprotein. Collectively, our work reveals a distinct function and cellular localization for two CHI-like proteins, introduces a new variation of a hemoprotein fold, and suggests that ancestral CHI-like proteins were hemoproteins.


  • Organizational Affiliation
    • Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA; Morgridge Institute for Research, Madison, Wisconsin, USA.

Macromolecule Content 

  • Total Structure Weight: 27.37 kDa 
  • Atom Count: 2,013 
  • Modeled Residue Count: 241 
  • Deposited Residue Count: 248 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Altered inheritance of mitochondria protein 46, mitochondrial248Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: AIM46FMP34YHR199C
UniProt
Find proteins for P38885 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38885 
Go to UniProtKB:  P38885
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP38885
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AKG
(Subject of Investigation/LOI)

Query on AKG



Download:Ideal Coordinates CCD File
B [auth A]2-OXOGLUTARIC ACID
C5 H6 O5
KPGXRSRHYNQIFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.234 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.167 (Depositor), 0.167 (DCC) 
  • R-Value Observed: 0.174 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.87α = 90
b = 71.35β = 95.165
c = 40.22γ = 90
Software Package:
Software NamePurpose
Cootmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-22
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description