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

Eun Hye Lee, Kitaik Lee, Kwang Yeon Hwang

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5 Citations (Scopus)

Abstract

The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and iso-propylmalate (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.

Original languageEnglish
Pages (from-to)922-931
Number of pages10
JournalActa Crystallographica Section D: Biological Crystallography
Volume70
Issue number4
DOIs
Publication statusPublished - 2014 Apr 1

Fingerprint

Methanocaldococcus
Isomerases
Aconitate Hydratase
Catalytic Domain
Proteins
Cysteine
Enzymes
Hydro-Lyases
Protein S
Archaea
homoaconitate hydratase
Dehydration
Disulfides
Cluster Analysis
Binding Sites

Keywords

  • aconitase family
  • Fe-S cluster
  • homoaconitase
  • IPM isomerase
  • Methanococcus jannaschii

ASJC Scopus subject areas

  • Structural Biology

Cite this

@article{3eedd355dc914880a895aee0cdffabe5,
title = "Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii",
abstract = "The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and iso-propylmalate (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 {\AA} resolution, respectively, together with the structure of the large subunit of homoaconitase (MJ1003) at 2.5 {\AA} 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.",
keywords = "aconitase family, Fe-S cluster, homoaconitase, IPM isomerase, Methanococcus jannaschii",
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year = "2014",
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T1 - Structural characterization and comparison of the large subunits of IPM isomerase and homoaconitase from Methanococcus jannaschii

AU - Lee, Eun Hye

AU - Lee, Kitaik

AU - Hwang, Kwang Yeon

PY - 2014/4/1

Y1 - 2014/4/1

N2 - The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and iso-propylmalate (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.

AB - The aconitase family of proteins includes three classes of hydro-lyase enzymes: aconitases, homoaconitases and iso-propylmalate (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.

KW - aconitase family

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KW - Methanococcus jannaschii

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