Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.
Identifieur interne : 000203 ( Ncbi/Checkpoint ); précédent : 000202; suivant : 000204Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.
Auteurs : Kerstin S. Wendt [Allemagne] ; Iris Schall ; Robert Huber ; Wolfgang Buckel ; Uwe JacobSource :
- The EMBO journal [ 0261-4189 ] ; 2003.
Descripteurs français
- KwdFr :
- Bactéries anaérobies à Gram négatif (enzymologie), Biotine (métabolisme), Canaux ioniques (métabolisme), Carboxy-lyases (métabolisme), Cristallographie aux rayons X, Dimérisation, Modèles moléculaires, Pompes ioniques (métabolisme), Sites de fixation, Sodium (métabolisme), Structure tertiaire des protéines.
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Biotin, Carboxy-Lyases, Ion Channels, Ion Pumps, Sodium.
- enzymology : Gram-Negative Anaerobic Bacteria.
- Binding Sites, Crystallography, X-Ray, Dimerization, Models, Molecular, Protein Structure, Tertiary.
Abstract
Glutaconyl-CoA decarboxylase is a biotin-dependent ion pump whereby the free energy of the glutaconyl-CoA decarboxylation to crotonyl-CoA drives the electrogenic transport of sodium ions from the cytoplasm into the periplasm. Here we present the crystal structure of the decarboxylase subunit (Gcdalpha) from Acidaminococcus fermentans and its complex with glutaconyl-CoA. The active sites of the dimeric Gcdalpha lie at the two interfaces between the mono mers, whereas the N-terminal domain provides the glutaconyl-CoA-binding site and the C-terminal domain binds the biotinyllysine moiety. The Gcdalpha catalyses the transfer of carbon dioxide from glutaconyl-CoA to a biotin carrier (Gcdgamma) that subsequently is decarboxylated by the carboxybiotin decarboxylation site within the actual Na(+) pump (Gcdbeta). The analysis of the active site lead to a novel mechanism for the biotin-dependent carboxy transfer whereby biotin acts as general acid. Furthermore, we propose a holoenzyme assembly in which the water-filled central channel of the Gcdalpha dimer lies co-axial with the ion channel (Gcdbeta). The central channel is blocked by arginines against passage of sodium ions which might enter the central channel through two side channels.
DOI: 10.1093/emboj/cdg358
PubMed: 12853465
Affiliations:
Links toward previous steps (curation, corpus...)
- to stream PubMed, to step Corpus: 002446
- to stream PubMed, to step Curation: 002446
- to stream PubMed, to step Checkpoint: 002329
- to stream Ncbi, to step Merge: 000203
- to stream Ncbi, to step Curation: 000203
Links to Exploration step
pubmed:12853465Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.</title><author><name sortKey="Wendt, Kerstin S" sort="Wendt, Kerstin S" uniqKey="Wendt K" first="Kerstin S" last="Wendt">Kerstin S. Wendt</name><affiliation wicri:level="1"><nlm:affiliation>Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried</wicri:regionArea><wicri:noRegion>82152 Martinsried</wicri:noRegion><wicri:noRegion>82152 Martinsried</wicri:noRegion><wicri:noRegion>D-82152 Martinsried</wicri:noRegion></affiliation></author><author><name sortKey="Schall, Iris" sort="Schall, Iris" uniqKey="Schall I" first="Iris" last="Schall">Iris Schall</name></author><author><name sortKey="Huber, Robert" sort="Huber, Robert" uniqKey="Huber R" first="Robert" last="Huber">Robert Huber</name></author><author><name sortKey="Buckel, Wolfgang" sort="Buckel, Wolfgang" uniqKey="Buckel W" first="Wolfgang" last="Buckel">Wolfgang Buckel</name></author><author><name sortKey="Jacob, Uwe" sort="Jacob, Uwe" uniqKey="Jacob U" first="Uwe" last="Jacob">Uwe Jacob</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2003">2003</date><idno type="RBID">pubmed:12853465</idno><idno type="pmid">12853465</idno><idno type="doi">10.1093/emboj/cdg358</idno><idno type="wicri:Area/PubMed/Corpus">002446</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002446</idno><idno type="wicri:Area/PubMed/Curation">002446</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002446</idno><idno type="wicri:Area/PubMed/Checkpoint">002329</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">002329</idno><idno type="wicri:Area/Ncbi/Merge">000203</idno><idno type="wicri:Area/Ncbi/Curation">000203</idno><idno type="wicri:Area/Ncbi/Checkpoint">000203</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.</title><author><name sortKey="Wendt, Kerstin S" sort="Wendt, Kerstin S" uniqKey="Wendt K" first="Kerstin S" last="Wendt">Kerstin S. Wendt</name><affiliation wicri:level="1"><nlm:affiliation>Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried</wicri:regionArea><wicri:noRegion>82152 Martinsried</wicri:noRegion><wicri:noRegion>82152 Martinsried</wicri:noRegion><wicri:noRegion>D-82152 Martinsried</wicri:noRegion></affiliation></author><author><name sortKey="Schall, Iris" sort="Schall, Iris" uniqKey="Schall I" first="Iris" last="Schall">Iris Schall</name></author><author><name sortKey="Huber, Robert" sort="Huber, Robert" uniqKey="Huber R" first="Robert" last="Huber">Robert Huber</name></author><author><name sortKey="Buckel, Wolfgang" sort="Buckel, Wolfgang" uniqKey="Buckel W" first="Wolfgang" last="Buckel">Wolfgang Buckel</name></author><author><name sortKey="Jacob, Uwe" sort="Jacob, Uwe" uniqKey="Jacob U" first="Uwe" last="Jacob">Uwe Jacob</name></author></analytic><series><title level="j">The EMBO journal</title><idno type="ISSN">0261-4189</idno><imprint><date when="2003" type="published">2003</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Binding Sites</term><term>Biotin (metabolism)</term><term>Carboxy-Lyases (metabolism)</term><term>Crystallography, X-Ray</term><term>Dimerization</term><term>Gram-Negative Anaerobic Bacteria (enzymology)</term><term>Ion Channels (metabolism)</term><term>Ion Pumps (metabolism)</term><term>Models, Molecular</term><term>Protein Structure, Tertiary</term><term>Sodium (metabolism)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bactéries anaérobies à Gram négatif (enzymologie)</term><term>Biotine (métabolisme)</term><term>Canaux ioniques (métabolisme)</term><term>Carboxy-lyases (métabolisme)</term><term>Cristallographie aux rayons X</term><term>Dimérisation</term><term>Modèles moléculaires</term><term>Pompes ioniques (métabolisme)</term><term>Sites de fixation</term><term>Sodium (métabolisme)</term><term>Structure tertiaire des protéines</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Biotin</term><term>Carboxy-Lyases</term><term>Ion Channels</term><term>Ion Pumps</term><term>Sodium</term></keywords><keywords scheme="MESH" qualifier="enzymologie" xml:lang="fr"><term>Bactéries anaérobies à Gram négatif</term></keywords><keywords scheme="MESH" qualifier="enzymology" xml:lang="en"><term>Gram-Negative Anaerobic Bacteria</term></keywords><keywords scheme="MESH" qualifier="métabolisme" xml:lang="fr"><term>Biotine</term><term>Canaux ioniques</term><term>Carboxy-lyases</term><term>Pompes ioniques</term><term>Sodium</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Binding Sites</term><term>Crystallography, X-Ray</term><term>Dimerization</term><term>Models, Molecular</term><term>Protein Structure, Tertiary</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Cristallographie aux rayons X</term><term>Dimérisation</term><term>Modèles moléculaires</term><term>Sites de fixation</term><term>Structure tertiaire des protéines</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Glutaconyl-CoA decarboxylase is a biotin-dependent ion pump whereby the free energy of the glutaconyl-CoA decarboxylation to crotonyl-CoA drives the electrogenic transport of sodium ions from the cytoplasm into the periplasm. Here we present the crystal structure of the decarboxylase subunit (Gcdalpha) from Acidaminococcus fermentans and its complex with glutaconyl-CoA. The active sites of the dimeric Gcdalpha lie at the two interfaces between the mono mers, whereas the N-terminal domain provides the glutaconyl-CoA-binding site and the C-terminal domain binds the biotinyllysine moiety. The Gcdalpha catalyses the transfer of carbon dioxide from glutaconyl-CoA to a biotin carrier (Gcdgamma) that subsequently is decarboxylated by the carboxybiotin decarboxylation site within the actual Na(+) pump (Gcdbeta). The analysis of the active site lead to a novel mechanism for the biotin-dependent carboxy transfer whereby biotin acts as general acid. Furthermore, we propose a holoenzyme assembly in which the water-filled central channel of the Gcdalpha dimer lies co-axial with the ion channel (Gcdbeta). The central channel is blocked by arginines against passage of sodium ions which might enter the central channel through two side channels.</div></front></TEI><affiliations><list><country><li>Allemagne</li></country></list><tree><noCountry><name sortKey="Buckel, Wolfgang" sort="Buckel, Wolfgang" uniqKey="Buckel W" first="Wolfgang" last="Buckel">Wolfgang Buckel</name><name sortKey="Huber, Robert" sort="Huber, Robert" uniqKey="Huber R" first="Robert" last="Huber">Robert Huber</name><name sortKey="Jacob, Uwe" sort="Jacob, Uwe" uniqKey="Jacob U" first="Uwe" last="Jacob">Uwe Jacob</name><name sortKey="Schall, Iris" sort="Schall, Iris" uniqKey="Schall I" first="Iris" last="Schall">Iris Schall</name></noCountry><country name="Allemagne"><noRegion><name sortKey="Wendt, Kerstin S" sort="Wendt, Kerstin S" uniqKey="Wendt K" first="Kerstin S" last="Wendt">Kerstin S. Wendt</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Sante/explor/MersV1/Data/Ncbi/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000203 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd -nk 000203 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Sante
|area= MersV1
|flux= Ncbi
|étape= Checkpoint
|type= RBID
|clé= pubmed:12853465
|texte= Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase.
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/RBID.i -Sk "pubmed:12853465" \
| HfdSelect -Kh $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd \
| NlmPubMed2Wicri -a MersV1
| This area was generated with Dilib version V0.6.33. |  |