1v25: Difference between revisions

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-[[Image:1v25.gif|left|200px]]
- {{Structure
+==Crystal structure of tt0168 from Thermus thermophilus HB8==
-|PDB= 1v25 |SIZE=350|CAPTION= <scene name='initialview01'>1v25</scene>, resolution 2.30&Aring;
+<StructureSection load='1v25' size='340' side='right'caption='[[1v25]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
-|SITE=
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>
+<table><tr><td colspan='2'>[[1v25]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V25 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V25 FirstGlance]. <br>
-|ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Long-chain-fatty-acid--CoA_ligase Long-chain-fatty-acid--CoA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.2.1.3 6.2.1.3] </span>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.3&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ANP:PHOSPHOAMINOPHOSPHONIC+ACID-ADENYLATE+ESTER'>ANP</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</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=1v25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v25 OCA], [https://pdbe.org/1v25 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v25 RCSB], [https://www.ebi.ac.uk/pdbsum/1v25 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v25 ProSAT], [https://www.topsan.org/Proteins/RSGI/1v25 TOPSAN]</span></td></tr>
-|RELATEDENTRY=[[1v26|1V26]]
+</table>
-|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1v25 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v25 OCA], [http://www.ebi.ac.uk/pdbsum/1v25 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1v25 RCSB]</span>
+== Function ==
-}}
+[https://www.uniprot.org/uniprot/LCFCS_THET8 LCFCS_THET8] Catalyzes the esterification of a number of long chain fatty acids with CoA, resulting in the formation of long-chain fatty acyl-CoA. Myristate (C14) is the most efficiently processed fatty acid, followed by palmitate (C16). Also catalyzes the esterification of stearate (C18) and laurate (C12), but at lower efficiency. Does not catalyze the esterification of the unsaturated fatty acids mysteroleic and palmitoleic acids in vitro.<ref>PMID:15145952</ref>
+== Evolutionary Conservation ==
-'''Crystal structure of tt0168 from Thermus thermophilus HB8'''
+[[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/v2/1v25_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/main_output.php?pdb_ID=1v25 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
 Long chain fatty acyl-CoA synthetases are responsible for fatty acid degradation as well as physiological regulation of cellular functions via the production of long chain fatty acyl-CoA esters. We report the first crystal structures of long chain fatty acyl-CoA synthetase homodimer (LC-FACS) from Thermus thermophilus HB8 (ttLC-FACS), including complexes with the ATP analogue adenosine 5'-(beta,gamma-imido) triphosphate (AMP-PNP) and myristoyl-AMP. ttLC-FACS is a member of the adenylate forming enzyme superfamily that catalyzes the ATP-dependent acylation of fatty acid in a two-step reaction. The first reaction step was shown to propagate in AMP-PNP complex crystals soaked with myristate solution. Myristoyl-AMP was identified as the intermediate. The AMP-PNP and the myristoyl-AMP complex structures show an identical closed conformation of the small C-terminal domains, whereas the uncomplexed form shows a variety of open conformations. Upon ATP binding, the fatty acid-binding tunnel gated by an aromatic residue opens to the ATP-binding site. The gated fatty acid-binding tunnel appears only to allow one-way movement of the fatty acid during overall catalysis. The protein incorporates a hydrophobic branch from the fatty acid-binding tunnel that is responsible for substrate specificity. Based on these high resolution crystal structures, we propose a unidirectional Bi Uni Uni Bi Ping-Pong mechanism for the two-step acylation by ttLC-FACS.
-==About this Structure==
+Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer.,Hisanaga Y, Ago H, Nakagawa N, Hamada K, Ida K, Yamamoto M, Hori T, Arii Y, Sugahara M, Kuramitsu S, Yokoyama S, Miyano M J Biol Chem. 2004 Jul 23;279(30):31717-26. Epub 2004 May 15. PMID:15145952<ref>PMID:15145952</ref>
-V25 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V25 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Structural basis of the substrate-specific two-step catalysis of long chain fatty acyl-CoA synthetase dimer., Hisanaga Y, Ago H, Nakagawa N, Hamada K, Ida K, Yamamoto M, Hori T, Arii Y, Sugahara M, Kuramitsu S, Yokoyama S, Miyano M, J Biol Chem. 2004 Jul 23;279(30):31717-26. Epub 2004 May 15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15145952 15145952]
+</div>
-[[Category: Long-chain-fatty-acid--CoA ligase]]
+<div class="pdbe-citations 1v25" style="background-color:#fffaf0;"></div>
-[[Category: Single protein]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Thermus thermophilus]]
-[[Category: Ago, H.]]
+[[Category: Ago H]]
-[[Category: Arii, Y.]]
+[[Category: Arii Y]]
-[[Category: Hamada, K.]]
+[[Category: Hamada K]]
-[[Category: Hisanaga, Y.]]
+[[Category: Hisanaga Y]]
-[[Category: Hori, T.]]
+[[Category: Hori T]]
-[[Category: Ida, K.]]
+[[Category: Ida K]]
-[[Category: Kanda, H.]]
+[[Category: Kanda H]]
-[[Category: Kuramitsu, S.]]
+[[Category: Kuramitsu S]]
-[[Category: Miyano, M.]]
+[[Category: Miyano M]]
-[[Category: Nakatsu, T.]]
+[[Category: Nakatsu T]]
-[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
+[[Category: Sugahara M]]
-[[Category: Sugahara, M.]]
+[[Category: Yamamoto M]]
-[[Category: Yamamoto, M.]]
+[[Category: Yokoyama S]]
-[[Category: Yokoyama, S.]]
-[[Category: ligase]]
-[[Category: riken structural genomics/proteomics initiative]]
-[[Category: rsgi]]
-[[Category: structural genomic]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 00:18:26 2008''