2e5a: Difference between revisions

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[[Image:2e5a.jpg|left|200px]]


{{Structure
==Crystal Structure of Bovine Lipoyltransferase in Complex with Lipoyl-AMP==
|PDB= 2e5a |SIZE=350|CAPTION= <scene name='initialview01'>2e5a</scene>, resolution 2.10&Aring;
<StructureSection load='2e5a' size='340' side='right'caption='[[2e5a]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
|SITE=  
== Structural highlights ==
|LIGAND= <scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=LAQ:5&#39;-O-[(R)-({5-[(3R)-1,2-DITHIOLAN-3-YL]PENTANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>LAQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>
<table><tr><td colspan='2'>[[2e5a]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E5A OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2E5A FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.1&#8491;</td></tr>
|GENE= LIPT1 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 Bos taurus])
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACY:ACETIC+ACID'>ACY</scene>, <scene name='pdbligand=LAQ:5-O-[(R)-({5-[(3R)-1,2-DITHIOLAN-3-YL]PENTANOYL}OXY)(HYDROXY)PHOSPHORYL]ADENOSINE'>LAQ</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
|DOMAIN=
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2e5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e5a OCA], [https://pdbe.org/2e5a PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2e5a RCSB], [https://www.ebi.ac.uk/pdbsum/2e5a PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2e5a ProSAT]</span></td></tr>
|RELATEDENTRY=
</table>
|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2e5a FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2e5a OCA], [http://www.ebi.ac.uk/pdbsum/2e5a PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2e5a RCSB]</span>
== Function ==
}}
[https://www.uniprot.org/uniprot/LIPT_BOVIN LIPT_BOVIN] Catalyzes the transfer of the lipoyl group from lipoyl-AMP to the specific lysine residue of lipoyl domains of lipoate-dependent enzymes.
 
== Evolutionary Conservation ==
'''Crystal Structure of Bovine Lipoyltransferase in Complex with Lipoyl-AMP'''
[[Image:Consurf_key_small.gif|200px|right]]
 
Check<jmol>
 
  <jmolCheckbox>
==Overview==
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/e5/2e5a_consurf.spt"</scriptWhenChecked>
Lipoic acid is an essential cofactor of the alpha-ketoacid dehydrogenase complexes and the glycine cleavage system. It is covalently attached to a specific lysine residue of the subunit of the complexes. The bovine lipoyltransferase (bLT) catalyzes the lipoic acid attachment reaction using lipoyl-AMP as a substrate, forming a lipoylated protein and AMP. To gain insights into the reaction mechanism at the atomic level, we have determined the crystal structure of bLT at 2.10 A resolution. Unexpectedly, the purified recombinant bLT contains endogenous lipoyl-AMP. The structure of bLT consists of N-terminal and C-terminal domains, and lipoyl-AMP is bound to the active site in the N-terminal domain, adopting a U-shaped conformation. The lipoyl moiety is buried in the hydrophobic pocket, forming van der Waals interactions, and the AMP moiety forms numerous hydrogen bonds with bLT in another tunnel-like cavity. These interactions work together to expose the C10 atom of lipoyl-AMP to the surface of the bLT molecule. The carbonyl oxygen atom of lipoyl-AMP interacts with the invariant Lys135. The interaction might stimulate the positive charge of the C10 atom of lipoyl-AMP, and consequently facilitate the nucleophilic attack by the lysine residue of the lipoate-acceptor protein, accompanying the bond cleavage between the carbonyl group and the phosphate group. We discuss the structural differences between bLT and the lipoate-protein ligase A from Escherichia coli and Thermoplasma acidophilum. We further demonstrate that bLT in mitochondria also contains endogenous lipoylmononucleotide, being ready for the lipoylation of apoproteins.
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 
    <text>to colour the structure by Evolutionary Conservation</text>
==About this Structure==
  </jmolCheckbox>
2E5A is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2E5A OCA].  
</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=2e5a ConSurf].
 
<div style="clear:both"></div>
==Reference==
__TOC__
Crystal structure of bovine lipoyltransferase in complex with lipoyl-AMP., Fujiwara K, Hosaka H, Matsuda M, Okamura-Ikeda K, Motokawa Y, Suzuki M, Nakagawa A, Taniguchi H, J Mol Biol. 2007 Aug 3;371(1):222-34. Epub 2007 May 26. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17570395 17570395]
</StructureSection>
[[Category: Bos taurus]]
[[Category: Bos taurus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Fujiwara, K.]]
[[Category: Fujiwara K]]
[[Category: Hosaka, H.]]
[[Category: Hosaka H]]
[[Category: Matsuda, M.]]
[[Category: Matsuda M]]
[[Category: Nakagawa, A.]]
[[Category: Nakagawa A]]
[[Category: Suzuki, M.]]
[[Category: Suzuki M]]
[[Category: ligase]]
[[Category: lipoyl-amp]]
[[Category: lipoyltransferase]]
 
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 02:43:56 2008''
Retrieved from "https://proteopedia.org/2e5a"