2gb0: Difference between revisions

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OCA

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-[[Image:2gb0.gif|left|200px]]<br /><applet load="2gb0" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="2gb0, resolution 1.85&Aring;" />
-'''Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme'''<br />
-==Overview==
+==Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme==
-BACKGROUND: Monomeric sarcosine oxidases (MSOXs) are among the simplest, members of a recently recognized family of eukaryotic and prokaryotic, enzymes that catalyze similar oxidative reactions with various secondary, or tertiary amino acids and contain covalently bound flavins. Other, members of this family include heterotetrameric sarcosine oxidase, N-methyltryptophan oxidase and pipecolate oxidase. Mammalian sarcosine, dehydrogenase and dimethylglycine dehydrogenase may be more distantly, related family members. RESULTS: The X-ray crystal structure of MSOX from, Bacillus sp. B-0618, expressed in Escherichia coli, has been solved at 2.0, A resolution by multiwavelength anomalous dispersion (MAD) from crystals, of the selenomethionine-substituted enzyme. Fourteen selenium sites, belonging to two MSOX molecules in the asymmetric unit, were used for MAD, phasing and to define the local twofold symmetry axis for electron-density, averaging. The structures of the native enzyme and of two enzyme-inhibitor, complexes were also determined. CONCLUSIONS: MSOX is a two-domain protein, with an overall topology most similar to that of D-amino acid oxidase, with which it shares 14% sequence identity. The flavin ring is located in, a very basic environment, making contact with sidechains of arginine, lysine, histidine and the N-terminal end of a helix dipole. The flavin is, covalently attached through an 8alpha-S-cysteinyl linkage to Cys315 of the, catalytic domain. Covalent attachment is probably self-catalyzed through, interactions with the positive sidechains and the helix dipole. Substrate, binding is probably stabilized by hydrogen bonds between the substrate, carboxylate and two basic sidechains, Arg52 and Lys348, located above the, re face of the flavin ring.
+<StructureSection load='2gb0' size='340' side='right'caption='[[2gb0]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2gb0]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacb0 Bacb0]. This structure supersedes the now removed PDB entries [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1l9f 1l9f] and [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1b3m 1b3m]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GB0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GB0 FirstGlance]. <br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">soxA, sox ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=69000 BACB0])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Sarcosine_oxidase Sarcosine oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.3.1 1.5.3.1] </span></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=2gb0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gb0 OCA], [https://pdbe.org/2gb0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gb0 RCSB], [https://www.ebi.ac.uk/pdbsum/2gb0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gb0 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/MSOX_BACB0 MSOX_BACB0]] Catalyzes the oxidative demethylation of sarcosine. Can also oxidize other secondary amino acids such as N-methyl-L-alanine.[HAMAP-Rule:MF_00516]
+== 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/gb/2gb0_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=2gb0 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: Monomeric sarcosine oxidases (MSOXs) are among the simplest members of a recently recognized family of eukaryotic and prokaryotic enzymes that catalyze similar oxidative reactions with various secondary or tertiary amino acids and contain covalently bound flavins. Other members of this family include heterotetrameric sarcosine oxidase, N-methyltryptophan oxidase and pipecolate oxidase. Mammalian sarcosine dehydrogenase and dimethylglycine dehydrogenase may be more distantly related family members. RESULTS: The X-ray crystal structure of MSOX from Bacillus sp. B-0618, expressed in Escherichia coli, has been solved at 2.0 A resolution by multiwavelength anomalous dispersion (MAD) from crystals of the selenomethionine-substituted enzyme. Fourteen selenium sites, belonging to two MSOX molecules in the asymmetric unit, were used for MAD phasing and to define the local twofold symmetry axis for electron-density averaging. The structures of the native enzyme and of two enzyme-inhibitor complexes were also determined. CONCLUSIONS: MSOX is a two-domain protein with an overall topology most similar to that of D-amino acid oxidase, with which it shares 14% sequence identity. The flavin ring is located in a very basic environment, making contact with sidechains of arginine, lysine, histidine and the N-terminal end of a helix dipole. The flavin is covalently attached through an 8alpha-S-cysteinyl linkage to Cys315 of the catalytic domain. Covalent attachment is probably self-catalyzed through interactions with the positive sidechains and the helix dipole. Substrate binding is probably stabilized by hydrogen bonds between the substrate carboxylate and two basic sidechains, Arg52 and Lys348, located above the re face of the flavin ring.
-==About this Structure==
+Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme.,Trickey P, Wagner MA, Jorns MS, Mathews FS Structure. 1999 Mar 15;7(3):331-45. PMID:10368302<ref>PMID:10368302</ref>
-GB0 is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.] with PO4, CL and FAD as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entries 1L9F and 1B3M. Active as [http://en.wikipedia.org/wiki/Sarcosine_oxidase Sarcosine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.3.1 1.5.3.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2GB0 OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Monomeric sarcosine oxidase: structure of a covalently flavinylated amine oxidizing enzyme., Trickey P, Wagner MA, Jorns MS, Mathews FS, Structure. 1999 Mar 15;7(3):331-45. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=10368302 10368302]
+</div>
-[[Category: Bacillus sp.]]
+<div class="pdbe-citations 2gb0" style="background-color:#fffaf0;"></div>
+==See Also==
+*[[Sarcosine oxidase|Sarcosine oxidase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bacb0]]
+[[Category: Large Structures]]
 [[Category: Sarcosine oxidase]]
-[[Category: Single protein]]
+[[Category: Jorns, M S]]
-[[Category: Jorns, M.S.]]
+[[Category: Mathews, F S]]
-[[Category: Mathews, F.S.]]
+[[Category: Trickey, P]]
-[[Category: Trickey, P.]]
+[[Category: Wagner, M A]]
-[[Category: Wagner, M.A.]]
+[[Category: Flavoprotein oxidase]]
-[[Category: CL]]
+[[Category: Oxidoreductase]]
-[[Category: FAD]]
-[[Category: PO4]]
-[[Category: flavoprotein oxidase]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 11:05:14 2007''