1eli: Difference between revisions

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 <StructureSection load='1eli' size='340' side='right'caption='[[1eli]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1eli]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacb0 Bacb0]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ELI OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ELI FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1eli]] 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=1ELI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ELI FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>, <scene name='pdbligand=PYC:PYRROLE-2-CARBOXYLATE'>PYC</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]] 2&#8491;</td></tr>
-<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=MSE:SELENOMETHIONINE'>MSE</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene>, <scene name='pdbligand=PYC:PYRROLE-2-CARBOXYLATE'>PYC</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1b3m|1b3m]], [[1el5|1el5]], [[1el7|1el7]], [[1el8|1el8]], [[1el9|1el9]]</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=1eli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eli OCA], [https://pdbe.org/1eli PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1eli RCSB], [https://www.ebi.ac.uk/pdbsum/1eli PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1eli ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[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] </span></td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1eli FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1eli OCA], [http://pdbe.org/1eli PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1eli RCSB], [http://www.ebi.ac.uk/pdbsum/1eli PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1eli ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://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=1eli ConSurf].
 <div style="clear:both"></div>
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Monomeric sarcosine oxidase (MSOX) is an inducible bacterial flavoenzyme that catalyzes the oxidative demethylation of sarcosine (N-methylglycine) and contains covalently bound FAD [8alpha-(S-cysteinyl)FAD]. This paper describes the spectroscopic and thermodynamic properties of MSOX as well as the X-ray crystallographic characterization of three new enzyme.inhibitor complexes. MSOX stabilizes the anionic form of the oxidized flavin (pK(a) = 8.3 versus 10.4 with free FAD), forms a thermodynamically stable flavin radical, and stabilizes the anionic form of the radical (pK(a) &lt; 6 versus pK(a) = 8.3 with free FAD). MSOX forms a covalent flavin.sulfite complex, but there appears to be a significant kinetic barrier against complex formation. Active site binding determinants were probed in thermodynamic studies with various substrate analogues whose binding was found to perturb the flavin absorption spectrum and inhibit MSOX activity. The carboxyl group of sarcosine is essential for binding since none is observed with simple amines. The amino group of sarcosine is not essential, but binding affinity depends on the nature of the substitution (CH(3)XCH(2)CO(2)(-), X = CH(2) &lt; O &lt; S &lt; Se &lt; Te), an effect which has been attributed to differences in the strength of donor-pi interactions. MSOX probably binds the zwitterionic form of sarcosine, as judged by the spectrally similar complexes formed with dimethylthioacetate [(CH(3))(2)S(+)CH(2)CO(2)(-)] and dimethylglycine (K(d) = 20.5 and 17.4 mM, respectively) and by the crystal structure of the latter. The methyl group of sarcosine is not essential but does contribute to binding affinity. The methyl group contribution varied from -3.79 to -0.65 kcal/mol with CH(3)XCH(2)CO(2)(-) depending on the nature of the heteroatom (NH(2)(+) &gt; O &gt; S) and appeared to be inversely correlated with heteroatom electron density. Charge-transfer complexes are formed with MSOX and CH(3)XCH(2)CO(2)(-) when X = S, Se, or Te. An excellent linear correlation is observed between the energy of the charge transfer bands and the one-electron reduction potentials of the ligands. The presence of a sulfur, selenium, or telurium atom identically positioned with respect to the flavin ring is confirmed by X-ray crystallography, although the increased atomic radius of S &lt; Se &lt; Te appears to simultaneously favor an alternate binding position for the heavier atoms. Although L-proline is a poor substrate, aromatic heterocyclic carboxylates containing a five-membered ring and various heteroatoms (X = NH, O, S) are good ligands (K(d, X=NH) = 1.37 mM) and form charge-transfer complexes with MSOX. The energy of the charge-transfer bands (S &gt; O &gt;&gt; NH) is linearly correlated with the one-electron ionization potentials of the corresponding heterocyclic rings.
-Monomeric sarcosine oxidase: 1. Flavin reactivity and active site binding determinants.,Wagner MA, Trickey P, Chen ZW, Mathews FS, Jorns MS Biochemistry. 2000 Aug 1;39(30):8813-24. PMID:10913292<ref>PMID:10913292</ref>
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 1eli" 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: Trickey P]]
-[[Category: Trickey, P]]
+[[Category: Wagner MA]]
-[[Category: Wagner, M A]]
-[[Category: Flavoprotein]]
-[[Category: Oxidase]]
-[[Category: Oxidoreductase]]