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1pix

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[[Image:1pix.jpg|left|200px]]<br /><applet load="1pix" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1pix, resolution 2.2&Aring;" />
 
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'''Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase'''<br />
 
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==Overview==
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==Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase==
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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.
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<StructureSection load='1pix' size='340' side='right'caption='[[1pix]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[1pix]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Acidaminococcus_fermentans Acidaminococcus fermentans]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PIX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PIX FirstGlance]. <br>
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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].
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FMT:FORMIC+ACID'>FMT</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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==Reference==
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1pix FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pix OCA], [https://pdbe.org/1pix PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pix RCSB], [https://www.ebi.ac.uk/pdbsum/1pix PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pix ProSAT]</span></td></tr>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12853465 12853465]
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/GCDA_ACIFV GCDA_ACIFV] Decarboxylase subunit of the primary sodium pump glutaconyl-CoA decarboxylase (GCD).
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pi/1pix_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1pix ConSurf].
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<div style="clear:both"></div>
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__TOC__
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</StructureSection>
[[Category: Acidaminococcus fermentans]]
[[Category: Acidaminococcus fermentans]]
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[[Category: Glutaconyl-CoA decarboxylase]]
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[[Category: Large Structures]]
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[[Category: Single protein]]
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[[Category: Buckel W]]
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[[Category: Buckel, W.]]
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[[Category: Huber R]]
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[[Category: Huber, R.]]
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[[Category: Jacob U]]
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[[Category: Jacob, U.]]
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[[Category: Schall I]]
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[[Category: Schall, I.]]
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[[Category: Wendt KS]]
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[[Category: Wendt, K S.]]
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[[Category: FMT]]
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[[Category: SO4]]
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[[Category: biotin-dependent ion pump]]
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[[Category: carboxyltransferase]]
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[[Category: decarboxylase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:29:17 2008''
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Current revision

Crystal structure of the carboxyltransferase subunit of the bacterial ion pump glutaconyl-coenzyme A decarboxylase

PDB ID 1pix

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