1vz5: Difference between revisions

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-[[Image:1vz5.gif|left|200px]]
- {{Structure
+==Succinate Complex of AtsK==
-|PDB= 1vz5 |SIZE=350|CAPTION= <scene name='initialview01'>1vz5</scene>, resolution 2.15&Aring;
+<StructureSection load='1vz5' size='340' side='right'caption='[[1vz5]], [[Resolution|resolution]] 2.15&Aring;' scene=''>
-|SITE= <scene name='pdbsite=AC1:Sin+Binding+Site+For+Chain+D'>AC1</scene>
+== Structural highlights ==
-|LIGAND= <scene name='pdbligand=SIN:SUCCINIC ACID'>SIN</scene>
+<table><tr><td colspan='2'>[[1vz5]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VZ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1VZ5 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]] 2.15&#8491;</td></tr>
-|GENE=
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene></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=1vz5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1vz5 OCA], [https://pdbe.org/1vz5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1vz5 RCSB], [https://www.ebi.ac.uk/pdbsum/1vz5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1vz5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/ATSK_PSEPU ATSK_PSEPU] Catalyzes the oxigenolytic cleavage of 2-ethylhexyl sulfate (2-EHS) in the presence of alpha-ketoglutarate to yield 2-ethyl-hexanal and succinate, the decarboxylated form of alpha-ketoglutarate. It can accepte a wide range of alpha-keto acids including 2-oxo-valerate, 2-oxo-adipate, 2-oxo-octanoate, 3-methyl-2-oxo-butyrate, oxaloacetate-alpha-ketoadipate, and alpha-ketooctanoate. It can catalyze the cleavage of medium-chain alkyl sulfate esters such as butylsulfate, pentylsulfate, hexylsulfate, heptylsulfate, octylsulfate, nonylsulfate, decylsulfate and sodium dodecyl sulfate (SDS).<ref>PMID:10913158</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/vz/1vz5_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=1vz5 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The alkylsulfatase AtsK from Pseudomonas putida S-313 is a member of the non-heme iron(II)-alpha-ketoglutarate-dependent dioxygenase superfamily. In the initial step of their catalytic cycle, enzymes belonging to this widespread and versatile family coordinate molecular oxygen to the iron center in the active site. The subsequent decarboxylation of the cosubstrate alpha-ketoglutarate yields carbon dioxide, succinate, and a highly reactive ferryl (IV) species, which is required for substrate oxidation via a complex mechanism involving the transfer of radical species. Non-productive activation of oxygen may lead to harmful side reactions; therefore, such enzymes need an effective built-in protection mechanism. One of the ways of controlling undesired side reactions is the self-hydroxylation of an aromatic side chain, which leads to an irreversibly inactivated species. Here we describe the crystal structure of the alkylsulfatase AtsK in complexes with succinate and with Fe(II)/succinate. In the crystal structure of the AtsK-Fe(II)-succinate complex, the side chain of Tyr(168) is co-ordinated to the iron, suggesting that Tyr(168) is the target of enzyme self-hydroxylation. This is the first structural study of an Fe(II)-alpha-ketoglutarate-dependent dioxygenase that presents an aromatic side chain coordinated to the metal center, thus allowing structural insight into this protective mechanism of enzyme self-inactivation.
-'''SUCCINATE COMPLEX OF ATSK'''
+Succinate complex crystal structures of the alpha-ketoglutarate-dependent dioxygenase AtsK: steric aspects of enzyme self-hydroxylation.,Muller I, Stuckl C, Wakeley J, Kertesz M, Uson I J Biol Chem. 2005 Feb 18;280(7):5716-23. Epub 2004 Nov 12. PMID:15542595<ref>PMID:15542595</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 1vz5" style="background-color:#fffaf0;"></div>
-==Overview==
+==See Also==
-The alkylsulfatase AtsK from Pseudomonas putida S-313 is a member of the non-heme iron(II)-alpha-ketoglutarate-dependent dioxygenase superfamily. In the initial step of their catalytic cycle, enzymes belonging to this widespread and versatile family coordinate molecular oxygen to the iron center in the active site. The subsequent decarboxylation of the cosubstrate alpha-ketoglutarate yields carbon dioxide, succinate, and a highly reactive ferryl (IV) species, which is required for substrate oxidation via a complex mechanism involving the transfer of radical species. Non-productive activation of oxygen may lead to harmful side reactions; therefore, such enzymes need an effective built-in protection mechanism. One of the ways of controlling undesired side reactions is the self-hydroxylation of an aromatic side chain, which leads to an irreversibly inactivated species. Here we describe the crystal structure of the alkylsulfatase AtsK in complexes with succinate and with Fe(II)/succinate. In the crystal structure of the AtsK-Fe(II)-succinate complex, the side chain of Tyr(168) is co-ordinated to the iron, suggesting that Tyr(168) is the target of enzyme self-hydroxylation. This is the first structural study of an Fe(II)-alpha-ketoglutarate-dependent dioxygenase that presents an aromatic side chain coordinated to the metal center, thus allowing structural insight into this protective mechanism of enzyme self-inactivation.
+*[[Sulfatase 3D structures|Sulfatase 3D structures]]
+== References ==
-==About this Structure==
+<references/>
-VZ5 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Pseudomonas_putida Pseudomonas putida]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1VZ5 OCA].
+__TOC__
+</StructureSection>
-==Reference==
+[[Category: Large Structures]]
-Succinate complex crystal structures of the alpha-ketoglutarate-dependent dioxygenase AtsK: steric aspects of enzyme self-hydroxylation., Muller I, Stuckl C, Wakeley J, Kertesz M, Uson I, J Biol Chem. 2005 Feb 18;280(7):5716-23. Epub 2004 Nov 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15542595 15542595]
 [[Category: Pseudomonas putida]]
-[[Category: Single protein]]
+[[Category: Kertesz M]]
-[[Category: Kertesz, M.]]
+[[Category: Mueller I]]
-[[Category: Mueller, I.]]
+[[Category: Stueckl AC]]
-[[Category: Stueckl, A C.]]
+[[Category: Uson I]]
-[[Category: Uson, I.]]
-[[Category: SIN]]
-[[Category: alkylsulfatase]]
-[[Category: jelly roll]]
-[[Category: non-heme fe(ii) alphaketoglutarate dependent dioxygenase]]
-[[Category: oxidoreductase]]
-[[Category: self hydroxylation]]
-[[Category: sulfatase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 14:49:58 2008''