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Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold.

Identifieur interne : 002414 ( PubMed/Curation ); précédent : 002413; suivant : 002415

Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold.

Auteurs : Sangita C. Sinha [États-Unis] ; Barnali N. Chaudhuri ; John W. Burgner ; Galina Yakovleva ; V Jo Davisson ; Janet L. Smith

Source :

The Journal of biological chemistry [ 0021-9258 ] ; 2004.

RBID : pubmed:14724278

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Motifs, Amino Acid Sequence, Basidiomycota (metabolism), Binding Sites, Catalysis, Crystallography, X-Ray, Dimerization, Histidine (chemistry), Hydro-Lyases (chemistry), Hydrogen (chemistry), Magnesium (chemistry), Models, Molecular, Molecular Sequence Data, Multigene Family, Peptides (chemistry), Protein Conformation, Protein Folding, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Ultracentrifugation.
MESH :
- chemical , chemistry : Histidine, Hydro-Lyases, Hydrogen, Magnesium, Peptides.
- metabolism : Basidiomycota.
- Amino Acid Motifs, Amino Acid Sequence, Binding Sites, Catalysis, Crystallography, X-Ray, Dimerization, Models, Molecular, Molecular Sequence Data, Multigene Family, Protein Conformation, Protein Folding, Protein Structure, Quaternary, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Homology, Amino Acid, Ultracentrifugation.

Abstract

Imidazole glycerol-phosphate dehydratase (IGPD) catalyzes the sixth step of histidine biosynthesis. The enzyme is of fundamental biochemical interest, because it catalyzes removal of a non-acidic hydrogen atom in the dehydration reaction. It is also a potential target for development of herbicides. IGPD is a metalloenzyme in which transition metals induce aggregation and are required for catalysis. Addition of 1 equivalent of Mn(2+)/subunit is shown by analytical ultracentrifugation to induce the formation of 24-mers from trimeric IGPD. Two histidine-rich motifs may participate in metal binding and aggregation. The 2.3-A crystal structure of metal-free trimeric IGPD from the fungus Filobasidiella neoformans reveals a novel fold containing an internal repeat, apparently the result of gene duplication. The 95-residue alpha/beta half-domain occurs in a few other proteins, including the GHMP kinase superfamily (galacto-homoserine-mevalonate-phosphomevalonate), but duplication to form a compact domain has not been seen elsewhere. Conserved residues cluster at two types of sites in the trimer, each site containing a conserved histidine-rich motif. A model is proposed for the intact, active 24-mer in which all highly conserved residues, including the histidine-rich motifs in both the N- and C-terminal halves of the polypeptide, cluster at a common site between trimers. This site is a candidate for the active site and also for metal binding leading to aggregation of trimers. The structure provides a basis for further studies of enzyme function and mechanism and for development of more potent and specific herbicides.

DOI: 10.1074/jbc.M312733200
PubMed: 14724278

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Le document en format XML

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<author><name sortKey="Sinha, Sangita C" sort="Sinha, Sangita C" uniqKey="Sinha S" first="Sangita C" last="Sinha">Sangita C. Sinha</name>
<affiliation wicri:level="1"><nlm:affiliation>Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907, USA.</nlm:affiliation>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea>Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907</wicri:regionArea>
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<author><name sortKey="Chaudhuri, Barnali N" sort="Chaudhuri, Barnali N" uniqKey="Chaudhuri B" first="Barnali N" last="Chaudhuri">Barnali N. Chaudhuri</name>
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<author><name sortKey="Burgner, John W" sort="Burgner, John W" uniqKey="Burgner J" first="John W" last="Burgner">John W. Burgner</name>
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<author><name sortKey="Yakovleva, Galina" sort="Yakovleva, Galina" uniqKey="Yakovleva G" first="Galina" last="Yakovleva">Galina Yakovleva</name>
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<author><name sortKey="Davisson, V Jo" sort="Davisson, V Jo" uniqKey="Davisson V" first="V Jo" last="Davisson">V Jo Davisson</name>
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<term>Amino Acid Sequence</term>
<term>Basidiomycota (metabolism)</term>
<term>Binding Sites</term>
<term>Catalysis</term>
<term>Crystallography, X-Ray</term>
<term>Dimerization</term>
<term>Histidine (chemistry)</term>
<term>Hydro-Lyases (chemistry)</term>
<term>Hydrogen (chemistry)</term>
<term>Magnesium (chemistry)</term>
<term>Models, Molecular</term>
<term>Molecular Sequence Data</term>
<term>Multigene Family</term>
<term>Peptides (chemistry)</term>
<term>Protein Conformation</term>
<term>Protein Folding</term>
<term>Protein Structure, Quaternary</term>
<term>Protein Structure, Secondary</term>
<term>Protein Structure, Tertiary</term>
<term>Sequence Homology, Amino Acid</term>
<term>Ultracentrifugation</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Basidiomycota (métabolisme)</term>
<term>Catalyse</term>
<term>Conformation des protéines</term>
<term>Cristallographie aux rayons X</term>
<term>Dimérisation</term>
<term>Données de séquences moléculaires</term>
<term>Famille multigénique</term>
<term>Histidine ()</term>
<term>Hydro-lyases ()</term>
<term>Hydrogène ()</term>
<term>Magnésium ()</term>
<term>Modèles moléculaires</term>
<term>Motifs d'acides aminés</term>
<term>Peptides ()</term>
<term>Pliage des protéines</term>
<term>Similitude de séquences d'acides aminés</term>
<term>Sites de fixation</term>
<term>Structure quaternaire des protéines</term>
<term>Structure secondaire des protéines</term>
<term>Structure tertiaire des protéines</term>
<term>Séquence d'acides aminés</term>
<term>Ultracentrifugation</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Histidine</term>
<term>Hydro-Lyases</term>
<term>Hydrogen</term>
<term>Magnesium</term>
<term>Peptides</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Basidiomycota</term>
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</keywords>
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<term>Amino Acid Sequence</term>
<term>Binding Sites</term>
<term>Catalysis</term>
<term>Crystallography, X-Ray</term>
<term>Dimerization</term>
<term>Models, Molecular</term>
<term>Molecular Sequence Data</term>
<term>Multigene Family</term>
<term>Protein Conformation</term>
<term>Protein Folding</term>
<term>Protein Structure, Quaternary</term>
<term>Protein Structure, Secondary</term>
<term>Protein Structure, Tertiary</term>
<term>Sequence Homology, Amino Acid</term>
<term>Ultracentrifugation</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Catalyse</term>
<term>Conformation des protéines</term>
<term>Cristallographie aux rayons X</term>
<term>Dimérisation</term>
<term>Données de séquences moléculaires</term>
<term>Famille multigénique</term>
<term>Histidine</term>
<term>Hydro-lyases</term>
<term>Hydrogène</term>
<term>Magnésium</term>
<term>Modèles moléculaires</term>
<term>Motifs d'acides aminés</term>
<term>Peptides</term>
<term>Pliage des protéines</term>
<term>Similitude de séquences d'acides aminés</term>
<term>Sites de fixation</term>
<term>Structure quaternaire des protéines</term>
<term>Structure secondaire des protéines</term>
<term>Structure tertiaire des protéines</term>
<term>Séquence d'acides aminés</term>
<term>Ultracentrifugation</term>
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<front><div type="abstract" xml:lang="en">Imidazole glycerol-phosphate dehydratase (IGPD) catalyzes the sixth step of histidine biosynthesis. The enzyme is of fundamental biochemical interest, because it catalyzes removal of a non-acidic hydrogen atom in the dehydration reaction. It is also a potential target for development of herbicides. IGPD is a metalloenzyme in which transition metals induce aggregation and are required for catalysis. Addition of 1 equivalent of Mn(2+)/subunit is shown by analytical ultracentrifugation to induce the formation of 24-mers from trimeric IGPD. Two histidine-rich motifs may participate in metal binding and aggregation. The 2.3-A crystal structure of metal-free trimeric IGPD from the fungus Filobasidiella neoformans reveals a novel fold containing an internal repeat, apparently the result of gene duplication. The 95-residue alpha/beta half-domain occurs in a few other proteins, including the GHMP kinase superfamily (galacto-homoserine-mevalonate-phosphomevalonate), but duplication to form a compact domain has not been seen elsewhere. Conserved residues cluster at two types of sites in the trimer, each site containing a conserved histidine-rich motif. A model is proposed for the intact, active 24-mer in which all highly conserved residues, including the histidine-rich motifs in both the N- and C-terminal halves of the polypeptide, cluster at a common site between trimers. This site is a candidate for the active site and also for metal binding leading to aggregation of trimers. The structure provides a basis for further studies of enzyme function and mechanism and for development of more potent and specific herbicides.</div>
</front>
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<Abstract><AbstractText>Imidazole glycerol-phosphate dehydratase (IGPD) catalyzes the sixth step of histidine biosynthesis. The enzyme is of fundamental biochemical interest, because it catalyzes removal of a non-acidic hydrogen atom in the dehydration reaction. It is also a potential target for development of herbicides. IGPD is a metalloenzyme in which transition metals induce aggregation and are required for catalysis. Addition of 1 equivalent of Mn(2+)/subunit is shown by analytical ultracentrifugation to induce the formation of 24-mers from trimeric IGPD. Two histidine-rich motifs may participate in metal binding and aggregation. The 2.3-A crystal structure of metal-free trimeric IGPD from the fungus Filobasidiella neoformans reveals a novel fold containing an internal repeat, apparently the result of gene duplication. The 95-residue alpha/beta half-domain occurs in a few other proteins, including the GHMP kinase superfamily (galacto-homoserine-mevalonate-phosphomevalonate), but duplication to form a compact domain has not been seen elsewhere. Conserved residues cluster at two types of sites in the trimer, each site containing a conserved histidine-rich motif. A model is proposed for the intact, active 24-mer in which all highly conserved residues, including the histidine-rich motifs in both the N- and C-terminal halves of the polypeptide, cluster at a common site between trimers. This site is a candidate for the active site and also for metal binding leading to aggregation of trimers. The structure provides a basis for further studies of enzyme function and mechanism and for development of more potent and specific herbicides.</AbstractText>
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Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold.

Crystal structure of imidazole glycerol-phosphate dehydratase: duplication of an unusual fold.

Source :

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Abstract

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