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2ars

From Proteopedia

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Crystal structure of lipoate-protein ligase A From Thermoplasma acidophilum

Structural highlights

2ars is a 1 chain structure with sequence from Thermoplasma acidophilum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.04Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2ars"

@@ Line 1: / Line 1: @@
 ==Crystal structure of lipoate-protein ligase A From Thermoplasma acidophilum==
-<StructureSection load='2ars' size='340' side='right' caption='[[2ars]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
+<StructureSection load='2ars' size='340' side='right'caption='[[2ars]], [[Resolution|resolution]] 2.04&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2ars]] 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=2ARS OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2ARS FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2ars]] 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=2ARS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2ARS FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.04&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2art|2art]], [[2aru|2aru]]</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=2ars FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ars OCA], [https://pdbe.org/2ars PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2ars RCSB], [https://www.ebi.ac.uk/pdbsum/2ars PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2ars ProSAT]</span></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=2ars FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2ars OCA], [http://pdbe.org/2ars PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2ars RCSB], [http://www.ebi.ac.uk/pdbsum/2ars PDBsum]</span></td></tr>
 </table>
 == 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 ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ar/2ars_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ar/2ars_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
-</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/chain_selection.php?pdb_ID=2ata ConSurf].
+</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=2ars ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 33: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Ha, J Y]]
+[[Category: Large Structures]]
-[[Category: Kim, D J]]
+[[Category: Thermoplasma acidophilum]]
-[[Category: Kim, K H]]
+[[Category: Ha JY]]
-[[Category: Lee, H H]]
+[[Category: Kim DJ]]
-[[Category: Lee, S J]]
+[[Category: Kim KH]]
-[[Category: Suh, S W]]
+[[Category: Lee HH]]
-[[Category: Yoon, H J]]
+[[Category: Lee SJ]]
-[[Category: Ligase]]
+[[Category: Suh SW]]
+[[Category: Yoon HJ]]

2ars

From Proteopedia

Current revision

Crystal structure of lipoate-protein ligase A From Thermoplasma acidophilum

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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