MaghrebDataLibMedV2, Main, Exploration, bibRecord, 000299

Identification of a new oat β-amylase by functional proteomics.

Identifieur interne : 000299 ( Main/Exploration ); précédent : 000298; suivant : 000300

Identification of a new oat β-amylase by functional proteomics.

Auteurs : Nihed Ben Halima [Tunisie] ; Bassem Khemakhem [Tunisie] ; Imen Fendri [Tunisie] ; Hiroyuki Ogata [Japon] ; Patrick Baril [France] ; Chantal Pichon [France] ; Slim Abdelkafi [Tunisie]

Source :

Biochimica et biophysica acta [ 0006-3002 ] ; 2016.

RBID : pubmed:26455400

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Avena (enzymology), Avena (genetics), Base Sequence (MeSH), Chromatography, Liquid (MeSH), Crystallography, X-Ray (MeSH), DNA, Complementary (chemistry), DNA, Complementary (genetics), Electrophoresis, Polyacrylamide Gel (MeSH), Models, Molecular (MeSH), Molecular Sequence Data (MeSH), Phylogeny (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Plant Proteins (metabolism), Protein Structure, Secondary (MeSH), Protein Structure, Tertiary (MeSH), Proteomics (methods), Seeds (enzymology), Seeds (genetics), Sequence Analysis, DNA (MeSH), Sequence Homology, Amino Acid (MeSH), Tandem Mass Spectrometry (MeSH), beta-Amylase (chemistry), beta-Amylase (genetics), beta-Amylase (metabolism).
MESH :
- chemical , chemistry : DNA, Complementary, Plant Proteins, beta-Amylase.
- enzymology : Avena, Seeds.
- genetics : Avena, DNA, Complementary, Plant Proteins, Seeds, beta-Amylase.
- chemical , metabolism : Plant Proteins, beta-Amylase.
- methods : Proteomics.
- Amino Acid Sequence, Base Sequence, Chromatography, Liquid, Crystallography, X-Ray, Electrophoresis, Polyacrylamide Gel, Models, Molecular, Molecular Sequence Data, Phylogeny, Protein Structure, Secondary, Protein Structure, Tertiary, Sequence Analysis, DNA, Sequence Homology, Amino Acid, Tandem Mass Spectrometry.

Abstract

Oat (Avena sativa L.) seed extracts exhibited a high degree of catalytic activity including amylase activities. Proteins in the oat seed extracts were optimized for their amylolytic activities. Oat extract with amylolytic activity was separated by SDS-PAGE and a major protein band with an apparent molecular mass of 53 kDa was subjected to tryptic digestion. The generated amino acid sequences were analyzed by liquid chromatography–tandem mass spectrometry (LC/ESI/MS/MS) and database searches. These sequences were used to identify a partial cDNA from expressed sequence tags (ESTs) of A. sativa L. Based upon EST sequences, a predicted full-length gene was identified, with an open reading frame of 1464 bp encoding a protein of 488 amino acid residues (AsBAMY), with a theoretical molecular mass of 55 kDa identified as a β-amylase belonging to the plant β-amylase family. Primary structure of oat β-amylase (AsBAMY) protein indicated high similarity with other β-amylase from other cereals such as wheat (Triticum aestivum), barley (Hordeum vulgare), and rye (Secale cereale) with two conserved Glu residues (E184 and E378) assigned as the “putative” catalytic residues which would act as an acid and base pair in the catalytic process. In addition, a 3D-model of AsBAMY was built from known X-ray structures and sequence alignments. A similar core (β/α)8-barrel architecture was found in AsBAMY like the other cereal β-amylases with a specific location of the active site in a pocket-like cavity structure made at one end of this core (β/α)8-barrel domain suggesting an accessibility of the non-reducing end of the substrate and thus confirming the results of AsBAMY exo-acting hydrolase.

DOI: 10.1016/j.bbapap.2015.10.001
PubMed: 26455400

Affiliations:

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Le document en format XML

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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Sequence (MeSH)</term>
<term>Avena (enzymology)</term>
<term>Avena (genetics)</term>
<term>Base Sequence (MeSH)</term>
<term>Chromatography, Liquid (MeSH)</term>
<term>Crystallography, X-Ray (MeSH)</term>
<term>DNA, Complementary (chemistry)</term>
<term>DNA, Complementary (genetics)</term>
<term>Electrophoresis, Polyacrylamide Gel (MeSH)</term>
<term>Models, Molecular (MeSH)</term>
<term>Molecular Sequence Data (MeSH)</term>
<term>Phylogeny (MeSH)</term>
<term>Plant Proteins (chemistry)</term>
<term>Plant Proteins (genetics)</term>
<term>Plant Proteins (metabolism)</term>
<term>Protein Structure, Secondary (MeSH)</term>
<term>Protein Structure, Tertiary (MeSH)</term>
<term>Proteomics (methods)</term>
<term>Seeds (enzymology)</term>
<term>Seeds (genetics)</term>
<term>Sequence Analysis, DNA (MeSH)</term>
<term>Sequence Homology, Amino Acid (MeSH)</term>
<term>Tandem Mass Spectrometry (MeSH)</term>
<term>beta-Amylase (chemistry)</term>
<term>beta-Amylase (genetics)</term>
<term>beta-Amylase (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>ADN complémentaire (composition chimique)</term>
<term>ADN complémentaire (génétique)</term>
<term>Analyse de séquence d'ADN (MeSH)</term>
<term>Avena (enzymologie)</term>
<term>Avena (génétique)</term>
<term>Chromatographie en phase liquide (MeSH)</term>
<term>Cristallographie aux rayons X (MeSH)</term>
<term>Données de séquences moléculaires (MeSH)</term>
<term>Graines (enzymologie)</term>
<term>Graines (génétique)</term>
<term>Modèles moléculaires (MeSH)</term>
<term>Phylogenèse (MeSH)</term>
<term>Protéines végétales (composition chimique)</term>
<term>Protéines végétales (génétique)</term>
<term>Protéines végétales (métabolisme)</term>
<term>Protéomique (méthodes)</term>
<term>Similitude de séquences d'acides aminés (MeSH)</term>
<term>Spectrométrie de masse en tandem (MeSH)</term>
<term>Structure secondaire des protéines (MeSH)</term>
<term>Structure tertiaire des protéines (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Séquence nucléotidique (MeSH)</term>
<term>beta-Amylase (composition chimique)</term>
<term>beta-Amylase (génétique)</term>
<term>beta-Amylase (métabolisme)</term>
<term>Électrophorèse sur gel de polyacrylamide (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Complementary</term>
<term>Plant Proteins</term>
<term>beta-Amylase</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>ADN complémentaire</term>
<term>Protéines végétales</term>
<term>beta-Amylase</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Avena</term>
<term>Graines</term>
</keywords>
<keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Avena</term>
<term>Seeds</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Avena</term>
<term>DNA, Complementary</term>
<term>Plant Proteins</term>
<term>Seeds</term>
<term>beta-Amylase</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN complémentaire</term>
<term>Avena</term>
<term>Graines</term>
<term>Protéines végétales</term>
<term>beta-Amylase</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Plant Proteins</term>
<term>beta-Amylase</term>
</keywords>
<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Proteomics</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Protéines végétales</term>
<term>beta-Amylase</term>
</keywords>
<keywords scheme="MESH" qualifier="méthodes" xml:lang="fr"><term>Protéomique</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Base Sequence</term>
<term>Chromatography, Liquid</term>
<term>Crystallography, X-Ray</term>
<term>Electrophoresis, Polyacrylamide Gel</term>
<term>Models, Molecular</term>
<term>Molecular Sequence Data</term>
<term>Phylogeny</term>
<term>Protein Structure, Secondary</term>
<term>Protein Structure, Tertiary</term>
<term>Sequence Analysis, DNA</term>
<term>Sequence Homology, Amino Acid</term>
<term>Tandem Mass Spectrometry</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Analyse de séquence d'ADN</term>
<term>Chromatographie en phase liquide</term>
<term>Cristallographie aux rayons X</term>
<term>Données de séquences moléculaires</term>
<term>Modèles moléculaires</term>
<term>Phylogenèse</term>
<term>Similitude de séquences d'acides aminés</term>
<term>Spectrométrie de masse en tandem</term>
<term>Structure secondaire des protéines</term>
<term>Structure tertiaire des protéines</term>
<term>Séquence d'acides aminés</term>
<term>Séquence nucléotidique</term>
<term>Électrophorèse sur gel de polyacrylamide</term>
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<front><div type="abstract" xml:lang="en">Oat (Avena sativa L.) seed extracts exhibited a high degree of catalytic activity including amylase activities. Proteins in the oat seed extracts were optimized for their amylolytic activities. Oat extract with amylolytic activity was separated by SDS-PAGE and a major protein band with an apparent molecular mass of 53 kDa was subjected to tryptic digestion. The generated amino acid sequences were analyzed by liquid chromatography–tandem mass spectrometry (LC/ESI/MS/MS) and database searches. These sequences were used to identify a partial cDNA from expressed sequence tags (ESTs) of A. sativa L. Based upon EST sequences, a predicted full-length gene was identified, with an open reading frame of 1464 bp encoding a protein of 488 amino acid residues (AsBAMY), with a theoretical molecular mass of 55 kDa identified as a β-amylase belonging to the plant β-amylase family. Primary structure of oat β-amylase (AsBAMY) protein indicated high similarity with other β-amylase from other cereals such as wheat (Triticum aestivum), barley (Hordeum vulgare), and rye (Secale cereale) with two conserved Glu residues (E184 and E378) assigned as the “putative” catalytic residues which would act as an acid and base pair in the catalytic process. In addition, a 3D-model of AsBAMY was built from known X-ray structures and sequence alignments. A similar core (β/α)8-barrel architecture was found in AsBAMY like the other cereal β-amylases with a specific location of the active site in a pocket-like cavity structure made at one end of this core (β/α)8-barrel domain suggesting an accessibility of the non-reducing end of the substrate and thus confirming the results of AsBAMY exo-acting hydrolase.</div>
</front>
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<li>Tunisie</li>
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<region><li>Centre-Val de Loire</li>
<li>Région Centre</li>
<li>Région du Kansai</li>
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<settlement><li>Kyoto</li>
<li>Orléans</li>
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<tree><country name="Tunisie"><noRegion><name sortKey="Ben Halima, Nihed" sort="Ben Halima, Nihed" uniqKey="Ben Halima N" first="Nihed" last="Ben Halima">Nihed Ben Halima</name>
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<name sortKey="Abdelkafi, Slim" sort="Abdelkafi, Slim" uniqKey="Abdelkafi S" first="Slim" last="Abdelkafi">Slim Abdelkafi</name>
<name sortKey="Fendri, Imen" sort="Fendri, Imen" uniqKey="Fendri I" first="Imen" last="Fendri">Imen Fendri</name>
<name sortKey="Khemakhem, Bassem" sort="Khemakhem, Bassem" uniqKey="Khemakhem B" first="Bassem" last="Khemakhem">Bassem Khemakhem</name>
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<country name="Japon"><region name="Région du Kansai"><name sortKey="Ogata, Hiroyuki" sort="Ogata, Hiroyuki" uniqKey="Ogata H" first="Hiroyuki" last="Ogata">Hiroyuki Ogata</name>
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<country name="France"><region name="Région Centre"><name sortKey="Baril, Patrick" sort="Baril, Patrick" uniqKey="Baril P" first="Patrick" last="Baril">Patrick Baril</name>
</region>
<name sortKey="Pichon, Chantal" sort="Pichon, Chantal" uniqKey="Pichon C" first="Chantal" last="Pichon">Chantal Pichon</name>
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       | HfdSelect -Kh $EXPLOR_AREA/Data/Main/Exploration/biblio.hfd   \
       | NlmPubMed2Wicri -a MaghrebDataLibMedV2

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	Serveur sur les données et bibliothèques médicales au Maghreb (version finale)
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Serveur sur les données et bibliothèques médicales au Maghreb (version finale)

Identification of a new oat β-amylase by functional proteomics.

Identification of a new oat β-amylase by functional proteomics.

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