4KP2

Crystal structure of homoaconitase large subunit from methanococcus jannaschii (MJ1003)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.504 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii

Lee, E.H.Lee, K.Hwang, K.Y.

(2014) Acta Crystallogr.,Sect.D 70: 922-931

  • DOI: 10.1107/S1399004713033762
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and isopropylmalate (IPM) isomerases. They have a common Fe-S cluster-binding site and catalyze the isomerization of specific substrates by seq ...

    The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and isopropylmalate (IPM) isomerases. They have a common Fe-S cluster-binding site and catalyze the isomerization of specific substrates by sequential dehydration and hydration. The archaeon Methanococcus jannaschii contains two aconitase family proteins, IPM isomerase and homoaconitase, which have 50% sequence identity. These two enzymes are heterodimeric proteins composed of large and small subunits encoded by separate genes. Although structures have been reported for the small subunits of the two enzymes, the first structures of oxidized and reduced forms of the large subunit of IPM isomerase (ox-MJ0499 and red-MJ0499, respectively) from M. jannaschii are reported here at 1.8 and 2.7 Å resolution, respectively, together with the structure of the large subunit of homoaconitase (MJ1003) at 2.5 Å resolution. The structures of both proteins have unbound Fe-S clusters and contain a fourth cysteine in the active site. The active site of MJ1003 is homologous to that of aconitase, whereas MJ0499 has significant structural distortion at the active site compared with aconitase. In addition, significant large conformational changes were observed in the active site of red-MJ0499 when compared with ox-MJ0499. The active sites of the two proteins adopt two different states before changing to the Fe-S cluster-bound `activated' state observed in aconitase. MJ1003 has an `open' active site, which forms an active pocket for the cluster, while ox-MJ0499 has a `closed' active site, with four cysteines in disulfide bonds. These data will be helpful in understanding the biochemical mechanism of clustering of the Fe-S protein family.


    Organizational Affiliation

    Division of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong-5, Seongbuk-gu, Seoul 136-701, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Homoaconitase large subunit
A, B
441Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)Mutation(s): 0 
Gene Names: hacA
EC: 4.2.1.114
Find proteins for Q58409 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440))
Go to UniProtKB:  Q58409
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.504 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 68.325α = 90.00
b = 103.098β = 90.00
c = 112.922γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
REFMACrefinement
MOLREPphasing
HKL-2000data reduction
HKL-2000data collection
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-05-13 
  • Released Date: 2014-04-23 
  • Deposition Author(s): Hwang, K.Y., Lee, E.H.

Revision History 

  • Version 1.0: 2014-04-23
    Type: Initial release