3ad8: Difference between revisions

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-{{Seed}}
-[[Image:3ad8.jpg|left|200px]]
-<!--
+==Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with pyrrole 2-carboxylate==
-The line below this paragraph, containing "STRUCTURE_3ad8", creates the "Structure Box" on the page.
+<StructureSection load='3ad8' size='340' side='right'caption='[[3ad8]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3ad8]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Corynebacterium_sp._U-96 Corynebacterium sp. U-96]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AD8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AD8 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.2&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=PYC:PYRROLE-2-CARBOXYLATE'>PYC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr>
-{{STRUCTURE_3ad8|  PDB=3ad8  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3ad8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ad8 OCA], [https://pdbe.org/3ad8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ad8 RCSB], [https://www.ebi.ac.uk/pdbsum/3ad8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ad8 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q50LF0_9CORY Q50LF0_9CORY]
+== 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/ad/3ad8_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=3ad8 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We characterized the crystal structures of heterotetrameric sarcosine oxidase (SO) from Corynebacterium sp. U-96 complexed with methylthioacetate (MTA), pyrrole 2-carboxylate (PCA), and sulfite, and of sarcosine-reduced SO. SO comprises alpha, beta, gamma , and delta subunits; FAD and FMN cofactors; and a large internal cavity. MTA and PCA are sandwiched between the re-face of the FAD isoalloxazine ring and the beta subunit C-terminal residues. Reduction of flavin cofactors shifts the beta subunit Ala1 toward the alpha subunit Met55, forming a surface cavity at the oxygen-channel vestibule and rendering the beta subunit C-terminal residues mobile. We identified three channels connecting the cavity and the enzyme surface. Two of them exist in the intersubunit space between alpha and beta subunits, and the substrate sarcosine seems to enter the active site through either of these channels and reaches the re-side of the FAD isoalloxazine ring by traversing the mobile beta subunit C-terminal residues. The third channel goes through the alpha subunit and has a folinic acid-binding site, where the iminium intermediate is converted to Gly and either formaldehyde or, 5,10-methylenetetrahydrofolate. Oxygen molecules are probably located on the surface cavity and diffuse to the FMN isoalloxazine ring; the H(2)O(2) formed exits via the oxygen channel.
-===Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with pyrrole 2-carboxylate===
+Channeling and conformational changes in the heterotetrameric sarcosine oxidase from Corynebacterium sp. U-96.,Moriguchi T, Ida K, Hikima T, Ueno G, Yamamoto M, Suzuki H J Biochem. 2010 Aug 18. PMID:20675294<ref>PMID:20675294</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3ad8" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_20675294}}, adds the Publication Abstract to the page
+*[[Sarcosine oxidase|Sarcosine oxidase]]
-(as it appears on PubMed at http://www.pubmed.gov), where 20675294 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_20675294}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Corynebacterium sp. U-96]]
-AD8 is a 4 chains structure with sequences from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AD8 OCA].
+[[Category: Large Structures]]
+[[Category: Ida K]]
-==Reference==
+[[Category: Moriguchi T]]
-<ref group="xtra">PMID:20675294</ref><references group="xtra"/>
+[[Category: Suzuki H]]
-[[Category: Bacteria]]
-[[Category: Sarcosine oxidase]]
-[[Category: Ida, K.]]
-[[Category: Moriguchi, T.]]
-[[Category: Suzuki, H.]]
-[[Category: Ligand complex]]
-[[Category: Oxidoreductase]]
-[[Category: Sarcosine oxidase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Aug 25 08:52:38 2010''