Crystal structure of Agrobacterium tumefaciens aconitase X (apo-form)

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

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Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily.

Watanabe, S.Murase, Y.Watanabe, Y.Sakurai, Y.Tajima, K.

(2021) Commun Biol 4: 687-687

  • DOI: https://doi.org/10.1038/s42003-021-02147-5
  • Primary Citation of Related Structures:  
    7CNP, 7CNQ, 7CNR, 7CNS, 7D2R

  • PubMed Abstract: 

    Aconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnX Type-I ) and mevalonate 5-phosphate dehydratase (AcnX Type-II ), respectively. We herein elucidated the crystal structures of AcnX Type-I from Agrobacterium tumefaciens (AtAcnX) and AcnX Type-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.

  • Organizational Affiliation

    Department of Bioscience, Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, Japan. irab@agr.ehime-u.ac.jp.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cis-3-hydroxy-L-proline dehydratase
A, B, C
579Agrobacterium tumefaciensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.131α = 90
b = 73.15β = 101.39
c = 133.603γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-16
    Type: Initial release
  • Version 1.1: 2022-12-28
    Changes: Database references
  • Version 1.2: 2024-05-29
    Changes: Data collection