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2art

From Proteopedia

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[[Image:2art.gif|left|200px]]<br /><applet load="2art" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2art, resolution 2.40&Aring;" />
 
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'''Crystal structure of lipoate-protein ligase A bound with lipoyl-AMP'''<br />
 
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==Overview==
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==Crystal structure of lipoate-protein ligase A bound with lipoyl-AMP==
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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.
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<StructureSection load='2art' size='340' side='right'caption='[[2art]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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==About this Structure==
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<table><tr><td colspan='2'>[[2art]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ART OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ART FirstGlance]. <br>
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2ART is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermoplasma_acidophilum Thermoplasma acidophilum] with <scene name='pdbligand=MG:'>MG</scene>, <scene name='pdbligand=LPA:'>LPA</scene> and <scene name='pdbligand=AMP:'>AMP</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2ART 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]] 2.4&#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=AMP:ADENOSINE+MONOPHOSPHATE'>AMP</scene>, <scene name='pdbligand=LPA:LIPOIC+ACID'>LPA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=2art FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2art OCA], [https://pdbe.org/2art PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2art RCSB], [https://www.ebi.ac.uk/pdbsum/2art PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2art ProSAT]</span></td></tr>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16141198 16141198]
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</table>
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[[Category: Single protein]]
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== Function ==
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[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>
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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/ar/2art_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=2art ConSurf].
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<div style="clear:both"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
[[Category: Thermoplasma acidophilum]]
[[Category: Thermoplasma acidophilum]]
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[[Category: Ha, J Y.]]
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[[Category: Ha JY]]
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[[Category: Kim, D J.]]
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[[Category: Kim DJ]]
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[[Category: Kim, K H.]]
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[[Category: Kim KH]]
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[[Category: Lee, H H.]]
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[[Category: Lee HH]]
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[[Category: Lee, S J.]]
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[[Category: Lee SJ]]
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[[Category: Suh, S W.]]
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[[Category: Suh SW]]
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[[Category: Yoon, H J.]]
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[[Category: Yoon HJ]]
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[[Category: AMP]]
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[[Category: LPA]]
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[[Category: MG]]
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[[Category: ligase]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 16:30:19 2008''
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Current revision

Crystal structure of lipoate-protein ligase A bound with lipoyl-AMP

PDB ID 2art

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