GlutaredoxinV1, Main, Exploration, bibRecord, 000596

The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the NrdH-redoxin family.

Identifieur interne : 000596 ( Main/Exploration ); précédent : 000595; suivant : 000597

The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the NrdH-redoxin family.

Auteurs : Koen Van Laer [Belgique] ; Margarida Oliveira ; Khadija Wahni ; Joris Messens

Source :

Protein science : a publication of the Protein Society [ 1469-896X ] ; 2014.

RBID : pubmed:24243781

Descripteurs français

English descriptors

KwdEn :
- Amino Acid Sequence (MeSH), Binding Sites (MeSH), Catalytic Domain (MeSH), Cysteine (MeSH), DNA Repair (genetics), DNA Replication (genetics), Escherichia coli Proteins (chemistry), Escherichia coli Proteins (genetics), Glutaredoxins (chemistry), Hydrogen Bonding (MeSH), Mycobacterium tuberculosis (chemistry), Mycobacterium tuberculosis (genetics), Mycobacterium tuberculosis (metabolism), Oxidation-Reduction (MeSH), Protein Structure, Tertiary (MeSH), Thioredoxins (chemistry), Thioredoxins (genetics).
MESH :
- chemical , chemistry : Escherichia coli Proteins, Glutaredoxins, Thioredoxins.
- chemical , genetics : Escherichia coli Proteins, Thioredoxins.
- chemical : Cysteine.
- chemistry : Mycobacterium tuberculosis.
- genetics : DNA Repair, DNA Replication, Mycobacterium tuberculosis.
- metabolism : Mycobacterium tuberculosis.
- Amino Acid Sequence, Binding Sites, Catalytic Domain, Hydrogen Bonding, Oxidation-Reduction, Protein Structure, Tertiary.

Abstract

NrdH-redoxins shuffle electrons from the NADPH pool in the cell to Class Ib ribonucleotide reductases, which in turn provide the precursors for DNA replication and repair. NrdH-redoxins have a CVQC active site motif and belong to the thioredoxin-fold protein family. As for other thioredoxin-fold proteins, the pK(a) of the nucleophilic cysteine of NrdH-redoxins is of particular interest since it affects the catalytic reaction rate of the enzymes. Recently, the pK(a) value of this cysteine in Corynebacterium glutamicum and Mycobacterium tuberculosis NrdH-redoxins were determined, but structural insights explaining the relatively low pK(a) remained elusive. We subjected C. glutamicum NrdH-redoxin to an extensive molecular dynamics simulation to expose the factors regulating the pK(a) of the nucleophilic cysteine. We found that the nucleophilic cysteine receives three hydrogen bonds from residues within the CVQC active site motif. Additionally, a fourth hydrogen bond with a lysine located N-terminal of the active site further lowers the cysteine pK(a). However, site-directed mutagenesis data show that the major contribution to the lowering of the cysteine pK(a) comes from the positive charge of the lysine and not from the additional Lys-Cys hydrogen bond. In 12% of the NrdH-redoxin family, this lysine is replaced by an arginine that also lowers the cysteine pK(a). All together, the four hydrogen bonds and the electrostatic effect of a lysine or an arginine located N-terminally of the active site dynamically regulate the pK(a) of the nucleophilic cysteine in NrdH-redoxins.

DOI: 10.1002/pro.2397
PubMed: 24243781
PubMed Central: PMC3926748

Affiliations:

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Le document en format XML

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<term>Binding Sites (MeSH)</term>
<term>Catalytic Domain (MeSH)</term>
<term>Cysteine (MeSH)</term>
<term>DNA Repair (genetics)</term>
<term>DNA Replication (genetics)</term>
<term>Escherichia coli Proteins (chemistry)</term>
<term>Escherichia coli Proteins (genetics)</term>
<term>Glutaredoxins (chemistry)</term>
<term>Hydrogen Bonding (MeSH)</term>
<term>Mycobacterium tuberculosis (chemistry)</term>
<term>Mycobacterium tuberculosis (genetics)</term>
<term>Mycobacterium tuberculosis (metabolism)</term>
<term>Oxidation-Reduction (MeSH)</term>
<term>Protein Structure, Tertiary (MeSH)</term>
<term>Thioredoxins (chemistry)</term>
<term>Thioredoxins (genetics)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Cystéine (MeSH)</term>
<term>Domaine catalytique (MeSH)</term>
<term>Glutarédoxines (composition chimique)</term>
<term>Liaison hydrogène (MeSH)</term>
<term>Mycobacterium tuberculosis (composition chimique)</term>
<term>Mycobacterium tuberculosis (génétique)</term>
<term>Mycobacterium tuberculosis (métabolisme)</term>
<term>Oxydoréduction (MeSH)</term>
<term>Protéines Escherichia coli (composition chimique)</term>
<term>Protéines Escherichia coli (génétique)</term>
<term>Réparation de l'ADN (génétique)</term>
<term>Réplication de l'ADN (génétique)</term>
<term>Sites de fixation (MeSH)</term>
<term>Structure tertiaire des protéines (MeSH)</term>
<term>Séquence d'acides aminés (MeSH)</term>
<term>Thiorédoxines (composition chimique)</term>
<term>Thiorédoxines (génétique)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Escherichia coli Proteins</term>
<term>Glutaredoxins</term>
<term>Thioredoxins</term>
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<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Escherichia coli Proteins</term>
<term>Thioredoxins</term>
</keywords>
<keywords scheme="MESH" type="chemical" xml:lang="en"><term>Cysteine</term>
</keywords>
<keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Mycobacterium tuberculosis</term>
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<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Glutarédoxines</term>
<term>Mycobacterium tuberculosis</term>
<term>Protéines Escherichia coli</term>
<term>Thiorédoxines</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>DNA Repair</term>
<term>DNA Replication</term>
<term>Mycobacterium tuberculosis</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Mycobacterium tuberculosis</term>
<term>Protéines Escherichia coli</term>
<term>Réparation de l'ADN</term>
<term>Réplication de l'ADN</term>
<term>Thiorédoxines</term>
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<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Mycobacterium tuberculosis</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Mycobacterium tuberculosis</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Amino Acid Sequence</term>
<term>Binding Sites</term>
<term>Catalytic Domain</term>
<term>Hydrogen Bonding</term>
<term>Oxidation-Reduction</term>
<term>Protein Structure, Tertiary</term>
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<term>Domaine catalytique</term>
<term>Liaison hydrogène</term>
<term>Oxydoréduction</term>
<term>Sites de fixation</term>
<term>Structure tertiaire des protéines</term>
<term>Séquence d'acides aminés</term>
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<front><div type="abstract" xml:lang="en">NrdH-redoxins shuffle electrons from the NADPH pool in the cell to Class Ib ribonucleotide reductases, which in turn provide the precursors for DNA replication and repair. NrdH-redoxins have a CVQC active site motif and belong to the thioredoxin-fold protein family. As for other thioredoxin-fold proteins, the pK(a) of the nucleophilic cysteine of NrdH-redoxins is of particular interest since it affects the catalytic reaction rate of the enzymes. Recently, the pK(a) value of this cysteine in Corynebacterium glutamicum and Mycobacterium tuberculosis NrdH-redoxins were determined, but structural insights explaining the relatively low pK(a) remained elusive. We subjected C. glutamicum NrdH-redoxin to an extensive molecular dynamics simulation to expose the factors regulating the pK(a) of the nucleophilic cysteine. We found that the nucleophilic cysteine receives three hydrogen bonds from residues within the CVQC active site motif. Additionally, a fourth hydrogen bond with a lysine located N-terminal of the active site further lowers the cysteine pK(a). However, site-directed mutagenesis data show that the major contribution to the lowering of the cysteine pK(a) comes from the positive charge of the lysine and not from the additional Lys-Cys hydrogen bond. In 12% of the NrdH-redoxin family, this lysine is replaced by an arginine that also lowers the cysteine pK(a). All together, the four hydrogen bonds and the electrostatic effect of a lysine or an arginine located N-terminally of the active site dynamically regulate the pK(a) of the nucleophilic cysteine in NrdH-redoxins.</div>
</front>
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<ArticleTitle>The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the NrdH-redoxin family.</ArticleTitle>
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<Abstract><AbstractText>NrdH-redoxins shuffle electrons from the NADPH pool in the cell to Class Ib ribonucleotide reductases, which in turn provide the precursors for DNA replication and repair. NrdH-redoxins have a CVQC active site motif and belong to the thioredoxin-fold protein family. As for other thioredoxin-fold proteins, the pK(a) of the nucleophilic cysteine of NrdH-redoxins is of particular interest since it affects the catalytic reaction rate of the enzymes. Recently, the pK(a) value of this cysteine in Corynebacterium glutamicum and Mycobacterium tuberculosis NrdH-redoxins were determined, but structural insights explaining the relatively low pK(a) remained elusive. We subjected C. glutamicum NrdH-redoxin to an extensive molecular dynamics simulation to expose the factors regulating the pK(a) of the nucleophilic cysteine. We found that the nucleophilic cysteine receives three hydrogen bonds from residues within the CVQC active site motif. Additionally, a fourth hydrogen bond with a lysine located N-terminal of the active site further lowers the cysteine pK(a). However, site-directed mutagenesis data show that the major contribution to the lowering of the cysteine pK(a) comes from the positive charge of the lysine and not from the additional Lys-Cys hydrogen bond. In 12% of the NrdH-redoxin family, this lysine is replaced by an arginine that also lowers the cysteine pK(a). All together, the four hydrogen bonds and the electrostatic effect of a lysine or an arginine located N-terminally of the active site dynamically regulate the pK(a) of the nucleophilic cysteine in NrdH-redoxins.</AbstractText>
<CopyrightInformation>© 2013 The Protein Society.</CopyrightInformation>
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<tree><noCountry><name sortKey="Messens, Joris" sort="Messens, Joris" uniqKey="Messens J" first="Joris" last="Messens">Joris Messens</name>
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<country name="Belgique"><region name="Région de Bruxelles-Capitale"><name sortKey="Van Laer, Koen" sort="Van Laer, Koen" uniqKey="Van Laer K" first="Koen" last="Van Laer">Koen Van Laer</name>
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   |texte=   The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the NrdH-redoxin family.
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	Serveur d'exploration sur la glutarédoxine
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Serveur d'exploration sur la glutarédoxine

The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the NrdH-redoxin family.

The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the NrdH-redoxin family.

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