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'''Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase'''<br /> | '''Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase'''<br /> | ||
==Overview== | ==Overview== | ||
| - | Glutaconyl-CoA decarboxylase is a biotin-dependent ion pump whereby the | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 1PIX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Acidaminococcus_fermentans Acidaminococcus fermentans] with SO4 and FMT as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutaconyl-CoA_decarboxylase Glutaconyl-CoA decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.70 4.1.1.70] Full crystallographic information is available from [http:// | + | 1PIX is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Acidaminococcus_fermentans Acidaminococcus fermentans] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=FMT:'>FMT</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Glutaconyl-CoA_decarboxylase Glutaconyl-CoA decarboxylase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.1.1.70 4.1.1.70] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PIX OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Jacob, U.]] | [[Category: Jacob, U.]] | ||
[[Category: Schall, I.]] | [[Category: Schall, I.]] | ||
| - | [[Category: Wendt, K | + | [[Category: Wendt, K S.]] |
[[Category: FMT]] | [[Category: FMT]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
| Line 25: | Line 25: | ||
[[Category: decarboxylase]] | [[Category: decarboxylase]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:29:17 2008'' |
Revision as of 12:29, 21 February 2008
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Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase
Overview
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.
About this Structure
1PIX is a Single protein structure of sequence from Acidaminococcus fermentans with and as ligands. Active as Glutaconyl-CoA decarboxylase, with EC number 4.1.1.70 Full crystallographic information is available from OCA.
Reference
Crystal structure of the carboxyltransferase subunit of the bacterial sodium ion pump glutaconyl-coenzyme A decarboxylase., Wendt KS, Schall I, Huber R, Buckel W, Jacob U, EMBO J. 2003 Jul 15;22(14):3493-502. PMID:12853465
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