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| | ==Crystal structure of lipoate-protein ligase A bound with ATP== | | ==Crystal structure of lipoate-protein ligase A bound with ATP== |
| - | <StructureSection load='2aru' size='340' side='right' caption='[[2aru]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='2aru' size='340' side='right'caption='[[2aru]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2aru]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ARU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2aru]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/"thermoplasma_acidophila"_(sic)_darland_et_al._1970 "thermoplasma acidophila" (sic) darland et al. 1970]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ARU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ARU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ars|2ars]], [[2art|2art]]</td></tr> | + | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[2ars|2ars]], [[2art|2art]]</div></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TA0514 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</td></tr> | + | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">TA0514 ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=2303 "Thermoplasma acidophila" (sic) Darland et al. 1970])</td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aru OCA], [http://pdbe.org/2aru PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2aru RCSB], [http://www.ebi.ac.uk/pdbsum/2aru PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2aru ProSAT]</span></td></tr> | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2aru FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2aru OCA], [https://pdbe.org/2aru PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2aru RCSB], [https://www.ebi.ac.uk/pdbsum/2aru PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2aru ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/LPLAN_THEAC LPLAN_THEAC]] Part of a lipoate-protein ligase complex that catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes. Can also use octanoate as substrate.<ref>PMID:16141198</ref> <ref>PMID:19520844</ref> <ref>PMID:19594830</ref> | + | [[https://www.uniprot.org/uniprot/LPLAN_THEAC LPLAN_THEAC]] Part of a lipoate-protein ligase complex that catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes. Can also use octanoate as substrate.<ref>PMID:16141198</ref> <ref>PMID:19520844</ref> <ref>PMID:19594830</ref> |
| | == Evolutionary Conservation == | | == Evolutionary Conservation == |
| | [[Image:Consurf_key_small.gif|200px|right]] | | [[Image:Consurf_key_small.gif|200px|right]] |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| | + | [[Category: Large Structures]] |
| | [[Category: Ha, J Y]] | | [[Category: Ha, J Y]] |
| | [[Category: Kim, D J]] | | [[Category: Kim, D J]] |
| Structural highlights
Function
[LPLAN_THEAC] Part of a lipoate-protein ligase complex that catalyzes both the ATP-dependent activation of exogenously supplied lipoate to lipoyl-AMP and the transfer of the activated lipoyl onto the lipoyl domains of lipoate-dependent enzymes. Can also use octanoate as substrate.[1] [2] [3]
Evolutionary Conservation
Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.
Publication Abstract from PubMed
Lipoic acid is the covalently attached cofactor of several multi-component enzyme complexes that catalyze key metabolic reactions. Attachment of lipoic acid to the lipoyl-dependent enzymes is catalyzed by lipoate-protein ligases (LPLs). In Escherichia coli, two distinct enzymes lipoate-protein ligase A (LplA) and lipB-encoded lipoyltransferase (LipB) catalyze independent pathways for lipoylation of the target proteins. The reaction catalyzed by LplA occurs in two steps. First, LplA activates exogenously supplied lipoic acid at the expense of ATP to lipoyl-AMP. Next, it transfers the enzyme-bound lipoyl-AMP to the epsilon-amino group of a specific lysine residue of the lipoyl domain to give an amide linkage. To gain insight into the mechanism of action by LplA, we have determined the crystal structure of Thermoplasma acidophilum LplA in three forms: (i) the apo form; (ii) the ATP complex; and (iii) the lipoyl-AMP complex. The overall fold of LplA bears some resemblance to that of the biotinyl protein ligase module of the E. coli biotin holoenzyme synthetase/bio repressor (BirA). Lipoyl-AMP is bound deeply in the bifurcated pocket of LplA and adopts a U-shaped conformation. Only the phosphate group and part of the ribose sugar of lipoyl-AMP are accessible from the bulk solvent through a tunnel-like passage, whereas the rest of the activated intermediate is completely buried inside the active site pocket. This first view of the activated intermediate bound to LplA allowed us to propose a model of the complexes between Ta LplA and lipoyl domains, thus shedding light on the target protein/lysine residue specificity of LplA.
Crystal structure of lipoate-protein ligase A bound with the activated intermediate: insights into interaction with lipoyl domains.,Kim DJ, Kim KH, Lee HH, Lee SJ, Ha JY, Yoon HJ, Suh SW J Biol Chem. 2005 Nov 11;280(45):38081-9. Epub 2005 Sep 2. PMID:16141198[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kim DJ, Kim KH, Lee HH, Lee SJ, Ha JY, Yoon HJ, Suh SW. Crystal structure of lipoate-protein ligase A bound with the activated intermediate: insights into interaction with lipoyl domains. J Biol Chem. 2005 Nov 11;280(45):38081-9. Epub 2005 Sep 2. PMID:16141198 doi:10.1074/jbc.M507284200
- ↑ Christensen QH, Cronan JE. The Thermoplasma acidophilum LplA-LplB complex defines a new class of bipartite lipoate-protein ligases. J Biol Chem. 2009 Aug 7;284(32):21317-26. doi: 10.1074/jbc.M109.015016. Epub 2009, Jun 11. PMID:19520844 doi:http://dx.doi.org/10.1074/jbc.M109.015016
- ↑ Posner MG, Upadhyay A, Bagby S, Hough DW, Danson MJ. A unique lipoylation system in the Archaea. Lipoylation in Thermoplasma acidophilum requires two proteins. FEBS J. 2009 Aug;276(15):4012-22. doi: 10.1111/j.1742-4658.2009.07110.x. Epub, 2009 Jul 7. PMID:19594830 doi:http://dx.doi.org/10.1111/j.1742-4658.2009.07110.x
- ↑ Kim DJ, Kim KH, Lee HH, Lee SJ, Ha JY, Yoon HJ, Suh SW. Crystal structure of lipoate-protein ligase A bound with the activated intermediate: insights into interaction with lipoyl domains. J Biol Chem. 2005 Nov 11;280(45):38081-9. Epub 2005 Sep 2. PMID:16141198 doi:10.1074/jbc.M507284200
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