3m12: Difference between revisions

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 <StructureSection load='3m12' size='340' side='right'caption='[[3m12]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3m12]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacb0 Bacb0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M12 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3m12]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_sp._B-0618 Bacillus sp. B-0618]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M12 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></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[3m13|3m13]]</div></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></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=3m12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m12 OCA], [https://pdbe.org/3m12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m12 RCSB], [https://www.ebi.ac.uk/pdbsum/3m12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m12 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]
+[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]]
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 </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=3m12 ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Oxygen reduction and sarcosine oxidation in monomeric sarcosine oxidase (MSOX) occur at separate sites above the si- and re-faces, respectively, of the flavin ring. Mutagenesis studies implicate Lys265 as the oxygen activation site. Substitution of Lys265 with a neutral (Met, Gln, or Ala) or basic (Arg) residue results in an approximately 10(4)- or 250-fold decrease, respectively, in the reaction rate. The overall structure of MSOX and residue conformation in the sarcosine binding cavity are unaffected by replacement of Lys265 with Met or Arg. The side chain of Met265 exhibits the same configuration in each molecule of Lys265Met crystals and is nearly congruent with Lys265 in wild-type MSOX. The side chain of Arg265 is, however, dramatically shifted ( approximately 4-5 A) compared with Lys265, points in the opposite direction, and exhibits significant conformational variability between molecules of the same crystal. The major species in solutions of Lys265Arg is likely to contain a "flipped-out" Arg265 and exhibit negligible oxygen activation, similar to Lys265Met. The 400-fold higher oxygen reactivity observed with Lys265Arg is attributed to a minor (&lt;1%) "flipped-in" Arg265 conformer whose oxygen reactivity is similar to that of wild-type MSOX. A structural water (WAT1), found above the si-face of the flavin ring in all previously determined MSOX structures, is part of an apparent proton relay system that extends from FAD N(5) to bulk solvent. WAT1 is strikingly absent in Lys265Met and Lys265Arg, a feature that may account for the apparent kinetic stabilization of a reductive half-reaction intermediate that is detectable with the mutants but not wild-type MSOX.
-Structural Characterization of Mutations at the Oxygen Activation Site in Monomeric Sarcosine Oxidase .,Jorns MS, Chen ZW, Mathews FS Biochemistry. 2010 Apr 12. PMID:20353187<ref>PMID:20353187</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 3m12" style="background-color:#fffaf0;"></div>
 ==See Also==
 *[[Sarcosine oxidase|Sarcosine oxidase]]
-== References ==
-<references/>
 __TOC__
 </StructureSection>
-[[Category: Bacb0]]
+[[Category: Bacillus sp. B-0618]]
 [[Category: Large Structures]]
-[[Category: Sarcosine oxidase]]
+[[Category: Chen Z-W]]
-[[Category: Chen, Z W]]
+[[Category: Jorns MS]]
-[[Category: Jorns, M S]]
+[[Category: Mathews FS]]
-[[Category: Mathews, F S]]
-[[Category: Cytoplasm]]
-[[Category: Fad]]
-[[Category: Flavoprotein]]
-[[Category: Flavoprotein oxidase]]
-[[Category: Oxidoreductase]]