6M09

The ligand-free structure of the chloroplast protein At3g03890

  • Classification: PLANT PROTEIN
  • Organism(s): Arabidopsis thaliana
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2020-02-20 Released: 2020-12-16 
  • Deposition Author(s): Wang, J., Liu, L.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

The Arabidopsis locus AT3G03890 encodes a dimeric beta-barrel protein implicated in heme degradation.

Wang, J.Guo, Q.Li, X.Wang, X.Liu, L.

(2020) Biochem J 

  • DOI: https://doi.org/10.1042/BCJ20200712
  • Primary Citation of Related Structures:  
    6M09, 6M0A

  • PubMed Abstract: 

    Plant tetrapyrroles, including heme and bilins, are synthesized in plastids. Heme oxygenase (HO) catalyzes the oxidative cleavage of heme to the linear tetrapyrrole biliverdin as the initial step in bilin biosynthesis. Besides the canonical α-helical HO that is conserved from prokaryotes to human, a subfamily of non-canonical dimeric β-barrel HO has been found in bacteria. In this work, we discovered that the Arabidopsis locus AT3G03890 encodes a dimeric β-barrel protein that is structurally related to the putative non-canonical HO and is located in chloroplasts. The recombinant protein was able to bind and degrade heme in a manner different from known HO proteins. Crystal structure of the heme-protein complex reveals that the heme-binding site is in the interdimer interface and the heme iron is coordinated by a fixed water molecule. Our results identify a new protein that may function additionally in the tetrapyrrole biosynthetic pathway.


  • Organizational Affiliation

    IBCAS, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AT3G03890 protein
A, B, C, D
292Arabidopsis thalianaMutation(s): 0 
Gene Names: At3g03890F20H23.6F20H23_6
UniProt
Find proteins for Q8LDU1 (Arabidopsis thaliana)
Explore Q8LDU1 
Go to UniProtKB:  Q8LDU1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LDU1
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.93α = 99.63
b = 79.964β = 109.8
c = 80.151γ = 104.48
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0503703
National Natural Science Foundation of China (NSFC)China31370759

Revision History  (Full details and data files)

  • Version 1.0: 2020-12-16
    Type: Initial release
  • Version 1.1: 2023-11-29
    Changes: Data collection, Database references, Refinement description