DetoxFungiV1, Main, Exploration, bibRecord, 002088

Ligand binding to truncated hemoglobin N from Mycobacterium tuberculosis is strongly modulated by the interplay between the distal heme pocket residues and internal water.

Identifieur interne : 002088 ( Main/Exploration ); précédent : 002087; suivant : 002089

Ligand binding to truncated hemoglobin N from Mycobacterium tuberculosis is strongly modulated by the interplay between the distal heme pocket residues and internal water.

Auteurs : Yannick H. Ouellet [Canada] ; Richard Daigle ; Patrick Lagüe ; David Dantsker ; Mario Milani ; Martino Bolognesi ; Joel M. Friedman ; Michel Guertin

Source :

The Journal of biological chemistry [ 0021-9258 ] ; 2008.

RBID : pubmed:18676995

Descripteurs français

English descriptors

KwdEn :
- Animals (MeSH), Bacterial Proteins (chemistry), Bacterial Proteins (genetics), Bacterial Proteins (metabolism), Binding Sites (MeSH), Heme (chemistry), Heme (genetics), Heme (metabolism), Horses (genetics), Horses (metabolism), Hydrogen Bonding (MeSH), Iron (chemistry), Iron (metabolism), Kinetics (MeSH), Ligands (MeSH), Mutation (MeSH), Mycobacterium tuberculosis (chemistry), Mycobacterium tuberculosis (genetics), Mycobacterium tuberculosis (metabolism), Myoglobin (chemistry), Myoglobin (genetics), Myoglobin (metabolism), Nitrates (chemistry), Nitrates (metabolism), Nitric Oxide (chemistry), Nitric Oxide (metabolism), Oxidation-Reduction (MeSH), Structure-Activity Relationship (MeSH), Truncated Hemoglobins (chemistry), Truncated Hemoglobins (genetics), Truncated Hemoglobins (metabolism), Water (chemistry), Water (metabolism).
MESH :
- chemical , chemistry : Bacterial Proteins, Heme, Iron, Myoglobin, Nitrates, Nitric Oxide, Truncated Hemoglobins, Water.
- chemical , genetics : Bacterial Proteins, Heme, Myoglobin, Truncated Hemoglobins.
- chemical , metabolism : Bacterial Proteins, Heme, Iron, Myoglobin, Nitrates, Nitric Oxide, Truncated Hemoglobins, Water.
- chemistry : Mycobacterium tuberculosis.
- genetics : Horses, Mycobacterium tuberculosis.
- metabolism : Horses, Mycobacterium tuberculosis.
- Animals, Binding Sites, Hydrogen Bonding, Kinetics, Ligands, Mutation, Oxidation-Reduction, Structure-Activity Relationship.

Abstract

The survival of Mycobacterium tuberculosis requires detoxification of host *NO. Oxygenated Mycobacterium tuberculosis truncated hemoglobin N catalyzes the rapid oxidation of nitric oxide to innocuous nitrate with a second-order rate constant (k'(NOD) approximately 745 x 10(6) m(-1) x s(-1)), which is approximately 15-fold faster than the reaction of horse heart myoglobin. We ask what aspects of structure and/or dynamics give rise to this enhanced reactivity. A first step is to expose what controls ligand/substrate binding to the heme. We present evidence that the main barrier to ligand binding to deoxy-truncated hemoglobin N (deoxy-trHbN) is the displacement of a distal cavity water molecule, which is mainly stabilized by residue Tyr(B10) but not coordinated to the heme iron. As observed in the Tyr(B10)/Gln(E11) apolar mutants, once this kinetic barrier is lowered, CO and O(2) binding is very rapid with rates approaching 1-2 x 10(9) m(-1) x s(-1). These large values almost certainly represent the upper limit for ligand binding to a heme protein and also indicate that the iron atom in trHbN is highly reactive. Kinetic measurements on the photoproduct of the *NO derivative of met-trHbN, where both the *NO and water can be directly followed, revealed that water rebinding is quite fast (approximately 1.49 x 10(8) s(-1)) and is responsible for the low geminate yield in trHbN. Molecular dynamics simulations, performed with trHbN and its distal mutants, indicated that in the absence of a distal water molecule, ligand access to the heme iron is not hindered. They also showed that a water molecule is stabilized next to the heme iron through hydrogen-bonding with Tyr(B10) and Gln(E11).

DOI: 10.1074/jbc.M804215200
PubMed: 18676995
PubMed Central: PMC2556007

Affiliations:

Links toward previous steps (curation, corpus...)

to stream Main, to step Corpus: 002067
to stream Main, to step Curation: 002067

Le document en format XML

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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals (MeSH)</term>
<term>Bacterial Proteins (chemistry)</term>
<term>Bacterial Proteins (genetics)</term>
<term>Bacterial Proteins (metabolism)</term>
<term>Binding Sites (MeSH)</term>
<term>Heme (chemistry)</term>
<term>Heme (genetics)</term>
<term>Heme (metabolism)</term>
<term>Horses (genetics)</term>
<term>Horses (metabolism)</term>
<term>Hydrogen Bonding (MeSH)</term>
<term>Iron (chemistry)</term>
<term>Iron (metabolism)</term>
<term>Kinetics (MeSH)</term>
<term>Ligands (MeSH)</term>
<term>Mutation (MeSH)</term>
<term>Mycobacterium tuberculosis (chemistry)</term>
<term>Mycobacterium tuberculosis (genetics)</term>
<term>Mycobacterium tuberculosis (metabolism)</term>
<term>Myoglobin (chemistry)</term>
<term>Myoglobin (genetics)</term>
<term>Myoglobin (metabolism)</term>
<term>Nitrates (chemistry)</term>
<term>Nitrates (metabolism)</term>
<term>Nitric Oxide (chemistry)</term>
<term>Nitric Oxide (metabolism)</term>
<term>Oxidation-Reduction (MeSH)</term>
<term>Structure-Activity Relationship (MeSH)</term>
<term>Truncated Hemoglobins (chemistry)</term>
<term>Truncated Hemoglobins (genetics)</term>
<term>Truncated Hemoglobins (metabolism)</term>
<term>Water (chemistry)</term>
<term>Water (metabolism)</term>
</keywords>
<keywords scheme="KwdFr" xml:lang="fr"><term>Animaux (MeSH)</term>
<term>Cinétique (MeSH)</term>
<term>Eau (composition chimique)</term>
<term>Eau (métabolisme)</term>
<term>Equus caballus (génétique)</term>
<term>Equus caballus (métabolisme)</term>
<term>Fer (composition chimique)</term>
<term>Fer (métabolisme)</term>
<term>Hème (composition chimique)</term>
<term>Hème (génétique)</term>
<term>Hème (métabolisme)</term>
<term>Hémoglobines tronquées (composition chimique)</term>
<term>Hémoglobines tronquées (génétique)</term>
<term>Hémoglobines tronquées (métabolisme)</term>
<term>Liaison hydrogène (MeSH)</term>
<term>Ligands (MeSH)</term>
<term>Monoxyde d'azote (composition chimique)</term>
<term>Monoxyde d'azote (métabolisme)</term>
<term>Mutation (MeSH)</term>
<term>Mycobacterium tuberculosis (composition chimique)</term>
<term>Mycobacterium tuberculosis (génétique)</term>
<term>Mycobacterium tuberculosis (métabolisme)</term>
<term>Myoglobine (composition chimique)</term>
<term>Myoglobine (génétique)</term>
<term>Myoglobine (métabolisme)</term>
<term>Nitrates (composition chimique)</term>
<term>Nitrates (métabolisme)</term>
<term>Oxydoréduction (MeSH)</term>
<term>Protéines bactériennes (composition chimique)</term>
<term>Protéines bactériennes (génétique)</term>
<term>Protéines bactériennes (métabolisme)</term>
<term>Relation structure-activité (MeSH)</term>
<term>Sites de fixation (MeSH)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Bacterial Proteins</term>
<term>Heme</term>
<term>Iron</term>
<term>Myoglobin</term>
<term>Nitrates</term>
<term>Nitric Oxide</term>
<term>Truncated Hemoglobins</term>
<term>Water</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Bacterial Proteins</term>
<term>Heme</term>
<term>Myoglobin</term>
<term>Truncated Hemoglobins</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Bacterial Proteins</term>
<term>Heme</term>
<term>Iron</term>
<term>Myoglobin</term>
<term>Nitrates</term>
<term>Nitric Oxide</term>
<term>Truncated Hemoglobins</term>
<term>Water</term>
</keywords>
<keywords scheme="MESH" qualifier="chemistry" xml:lang="en"><term>Mycobacterium tuberculosis</term>
</keywords>
<keywords scheme="MESH" qualifier="composition chimique" xml:lang="fr"><term>Eau</term>
<term>Fer</term>
<term>Hème</term>
<term>Hémoglobines tronquées</term>
<term>Monoxyde d'azote</term>
<term>Mycobacterium tuberculosis</term>
<term>Myoglobine</term>
<term>Nitrates</term>
<term>Protéines bactériennes</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Horses</term>
<term>Mycobacterium tuberculosis</term>
</keywords>
<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Equus caballus</term>
<term>Hème</term>
<term>Hémoglobines tronquées</term>
<term>Mycobacterium tuberculosis</term>
<term>Myoglobine</term>
<term>Protéines bactériennes</term>
</keywords>
<keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Horses</term>
<term>Mycobacterium tuberculosis</term>
</keywords>
<keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Eau</term>
<term>Equus caballus</term>
<term>Fer</term>
<term>Hème</term>
<term>Hémoglobines tronquées</term>
<term>Monoxyde d'azote</term>
<term>Mycobacterium tuberculosis</term>
<term>Myoglobine</term>
<term>Nitrates</term>
<term>Protéines bactériennes</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Animals</term>
<term>Binding Sites</term>
<term>Hydrogen Bonding</term>
<term>Kinetics</term>
<term>Ligands</term>
<term>Mutation</term>
<term>Oxidation-Reduction</term>
<term>Structure-Activity Relationship</term>
</keywords>
<keywords scheme="MESH" xml:lang="fr"><term>Animaux</term>
<term>Cinétique</term>
<term>Liaison hydrogène</term>
<term>Ligands</term>
<term>Mutation</term>
<term>Oxydoréduction</term>
<term>Relation structure-activité</term>
<term>Sites de fixation</term>
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<front><div type="abstract" xml:lang="en">The survival of Mycobacterium tuberculosis requires detoxification of host *NO. Oxygenated Mycobacterium tuberculosis truncated hemoglobin N catalyzes the rapid oxidation of nitric oxide to innocuous nitrate with a second-order rate constant (k'(NOD) approximately 745 x 10(6) m(-1) x s(-1)), which is approximately 15-fold faster than the reaction of horse heart myoglobin. We ask what aspects of structure and/or dynamics give rise to this enhanced reactivity. A first step is to expose what controls ligand/substrate binding to the heme. We present evidence that the main barrier to ligand binding to deoxy-truncated hemoglobin N (deoxy-trHbN) is the displacement of a distal cavity water molecule, which is mainly stabilized by residue Tyr(B10) but not coordinated to the heme iron. As observed in the Tyr(B10)/Gln(E11) apolar mutants, once this kinetic barrier is lowered, CO and O(2) binding is very rapid with rates approaching 1-2 x 10(9) m(-1) x s(-1). These large values almost certainly represent the upper limit for ligand binding to a heme protein and also indicate that the iron atom in trHbN is highly reactive. Kinetic measurements on the photoproduct of the *NO derivative of met-trHbN, where both the *NO and water can be directly followed, revealed that water rebinding is quite fast (approximately 1.49 x 10(8) s(-1)) and is responsible for the low geminate yield in trHbN. Molecular dynamics simulations, performed with trHbN and its distal mutants, indicated that in the absence of a distal water molecule, ligand access to the heme iron is not hindered. They also showed that a water molecule is stabilized next to the heme iron through hydrogen-bonding with Tyr(B10) and Gln(E11).</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">18676995</PMID>
<DateCompleted><Year>2008</Year>
<Month>11</Month>
<Day>04</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
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<JournalIssue CitedMedium="Print"><Volume>283</Volume>
<Issue>40</Issue>
<PubDate><Year>2008</Year>
<Month>Oct</Month>
<Day>03</Day>
</PubDate>
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<Title>The Journal of biological chemistry</Title>
<ISOAbbreviation>J Biol Chem</ISOAbbreviation>
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<ArticleTitle>Ligand binding to truncated hemoglobin N from Mycobacterium tuberculosis is strongly modulated by the interplay between the distal heme pocket residues and internal water.</ArticleTitle>
<Pagination><MedlinePgn>27270-8</MedlinePgn>
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<Abstract><AbstractText>The survival of Mycobacterium tuberculosis requires detoxification of host *NO. Oxygenated Mycobacterium tuberculosis truncated hemoglobin N catalyzes the rapid oxidation of nitric oxide to innocuous nitrate with a second-order rate constant (k'(NOD) approximately 745 x 10(6) m(-1) x s(-1)), which is approximately 15-fold faster than the reaction of horse heart myoglobin. We ask what aspects of structure and/or dynamics give rise to this enhanced reactivity. A first step is to expose what controls ligand/substrate binding to the heme. We present evidence that the main barrier to ligand binding to deoxy-truncated hemoglobin N (deoxy-trHbN) is the displacement of a distal cavity water molecule, which is mainly stabilized by residue Tyr(B10) but not coordinated to the heme iron. As observed in the Tyr(B10)/Gln(E11) apolar mutants, once this kinetic barrier is lowered, CO and O(2) binding is very rapid with rates approaching 1-2 x 10(9) m(-1) x s(-1). These large values almost certainly represent the upper limit for ligand binding to a heme protein and also indicate that the iron atom in trHbN is highly reactive. Kinetic measurements on the photoproduct of the *NO derivative of met-trHbN, where both the *NO and water can be directly followed, revealed that water rebinding is quite fast (approximately 1.49 x 10(8) s(-1)) and is responsible for the low geminate yield in trHbN. Molecular dynamics simulations, performed with trHbN and its distal mutants, indicated that in the absence of a distal water molecule, ligand access to the heme iron is not hindered. They also showed that a water molecule is stabilized next to the heme iron through hydrogen-bonding with Tyr(B10) and Gln(E11).</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ouellet</LastName>
<ForeName>Yannick H</ForeName>
<Initials>YH</Initials>
<AffiliationInfo><Affiliation>Department of Biochemistry and Microbiology, Laval University, Quebec, Canada, G1K 7P4.</Affiliation>
</AffiliationInfo>
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<ForeName>Richard</ForeName>
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<Author ValidYN="Y"><LastName>Lagüe</LastName>
<ForeName>Patrick</ForeName>
<Initials>P</Initials>
</Author>
<Author ValidYN="Y"><LastName>Dantsker</LastName>
<ForeName>David</ForeName>
<Initials>D</Initials>
</Author>
<Author ValidYN="Y"><LastName>Milani</LastName>
<ForeName>Mario</ForeName>
<Initials>M</Initials>
</Author>
<Author ValidYN="Y"><LastName>Bolognesi</LastName>
<ForeName>Martino</ForeName>
<Initials>M</Initials>
</Author>
<Author ValidYN="Y"><LastName>Friedman</LastName>
<ForeName>Joel M</ForeName>
<Initials>JM</Initials>
</Author>
<Author ValidYN="Y"><LastName>Guertin</LastName>
<ForeName>Michel</ForeName>
<Initials>M</Initials>
</Author>
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<Language>eng</Language>
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<Acronym>AI</Acronym>
<Agency>NIAID NIH HHS</Agency>
<Country>United States</Country>
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<Day>02</Day>
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<MedlineJournalInfo><Country>United States</Country>
<MedlineTA>J Biol Chem</MedlineTA>
<NlmUniqueID>2985121R</NlmUniqueID>
<ISSNLinking>0021-9258</ISSNLinking>
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<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D001426">Bacterial Proteins</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="C102539">GlbN protein, bacteria</NameOfSubstance>
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<Chemical><RegistryNumber>059QF0KO0R</RegistryNumber>
<NameOfSubstance UI="D014867">Water</NameOfSubstance>
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<Chemical><RegistryNumber>31C4KY9ESH</RegistryNumber>
<NameOfSubstance UI="D009569">Nitric Oxide</NameOfSubstance>
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<MeshHeadingList><MeshHeading><DescriptorName UI="D000818" MajorTopicYN="N">Animals</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001426" MajorTopicYN="N">Bacterial Proteins</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
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<MeshHeading><DescriptorName UI="D001665" MajorTopicYN="N">Binding Sites</DescriptorName>
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<MeshHeading><DescriptorName UI="D006418" MajorTopicYN="N">Heme</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006736" MajorTopicYN="N">Horses</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D006860" MajorTopicYN="N">Hydrogen Bonding</DescriptorName>
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<MeshHeading><DescriptorName UI="D007501" MajorTopicYN="N">Iron</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
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<MeshHeading><DescriptorName UI="D007700" MajorTopicYN="N">Kinetics</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008024" MajorTopicYN="N">Ligands</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009154" MajorTopicYN="N">Mutation</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009169" MajorTopicYN="N">Mycobacterium tuberculosis</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009211" MajorTopicYN="N">Myoglobin</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009566" MajorTopicYN="N">Nitrates</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D009569" MajorTopicYN="N">Nitric Oxide</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName>
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	Serveur d'exploration sur la détoxication des champignons
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Ligand binding to truncated hemoglobin N from Mycobacterium tuberculosis is strongly modulated by the interplay between the distal heme pocket residues and internal water.

Ligand binding to truncated hemoglobin N from Mycobacterium tuberculosis is strongly modulated by the interplay between the distal heme pocket residues and internal water.

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