4DOO | pdb_00004doo

Crystal structure of Arabidopsis thaliana fatty-acid binding protein At3g63170 (AtFAP1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.248 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.200 (Depositor), 0.201 (DCC) 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Evolution of the chalcone-isomerase fold from fatty-acid binding to stereospecific catalysis.

Ngaki, M.N.Louie, G.V.Philippe, R.N.Manning, G.Pojer, F.Bowman, M.E.Li, L.Larsen, E.Wurtele, E.S.Noel, J.P.

(2012) Nature 485: 530-533

  • DOI: https://doi.org/10.1038/nature11009
  • Primary Citation Related Structures: 
    4DOI, 4DOK, 4DOL, 4DOO

  • PubMed Abstract: 

    Specialized metabolic enzymes biosynthesize chemicals of ecological importance, often sharing a pedigree with primary metabolic enzymes. However, the lineage of the enzyme chalcone isomerase (CHI) remained unknown. In vascular plants, CHI-catalysed conversion of chalcones to chiral (S)-flavanones is a committed step in the production of plant flavonoids, compounds that contribute to attraction, defence and development. CHI operates near the diffusion limit with stereospecific control. Although associated primarily with plants, the CHI fold occurs in several other eukaryotic lineages and in some bacteria. Here we report crystal structures, ligand-binding properties and in vivo functional characterization of a non-catalytic CHI-fold family from plants. Arabidopsis thaliana contains five actively transcribed genes encoding CHI-fold proteins, three of which additionally encode amino-terminal chloroplast-transit sequences. These three CHI-fold proteins localize to plastids, the site of de novo fatty-acid biosynthesis in plant cells. Furthermore, their expression profiles correlate with those of core fatty-acid biosynthetic enzymes, with maximal expression occurring in seeds and coinciding with increased fatty-acid storage in the developing embryo. In vitro, these proteins are fatty-acid-binding proteins (FAPs). FAP knockout A. thaliana plants show elevated α-linolenic acid levels and marked reproductive defects, including aberrant seed formation. Notably, the FAP discovery defines the adaptive evolution of a stereospecific and catalytically 'perfected' enzyme from a non-enzymatic ancestor over a defined period of plant evolution.


  • Organizational Affiliation
    • Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa 50011, USA.

Macromolecule Content 

  • Total Structure Weight: 46.4 kDa 
  • Atom Count: 3,700 
  • Modeled Residue Count: 406 
  • Deposited Residue Count: 410 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chalcone-flavanone isomerase family protein
A, B
205Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g63170At3g63170/F16M2_20F16M2_20
UniProt
Find proteins for Q9M1X2 (Arabidopsis thaliana)
Explore Q9M1X2 
Go to UniProtKB:  Q9M1X2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9M1X2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.248 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.489α = 90
b = 56.901β = 90
c = 139.608γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-06-06
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations