1el9 - Revision history

OCA at 10:03, 20 March 2024

OCA — Wed, 20 Mar 2024 10:03:47 GMT

←Older revision		Revision as of 10:03, 20 March 2024
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	<StructureSection load='1el9' size='340' side='right'caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1el9' size='340' side='right'caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1el9]] 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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EL9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1el9]] 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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EL9 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=MTG:~~[~~METHYLTHIO~~]~~ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</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]] 2Å</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=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	~~<tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td><~~td class~~=~~"sblockDat"><div style~~=~~'overflow~~: ~~auto; max-height: 3em;~~'>~~[[1b3m\|1b3m]], [[1el5\|1el5]], [[1el7\|1el7]], [[1el8\|1el8]], [[1eli\|1eli]]~~</~~div~~><~~/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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [https://pdbe.org/1el9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [https://www.ebi.ac.uk/pdbsum/1el9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1el9 ProSAT]</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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [https://pdbe.org/1el9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [https://www.ebi.ac.uk/pdbsum/1el9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1el9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[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=1el9 ConSurf].		</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=1el9 ConSurf].
	<div style="clear:both"></div>		<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) < 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) < O < S < Se < 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)(+) > O > 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 < Se < 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 > O >> 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®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 1el9" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
	*[[Sarcosine oxidase\|Sarcosine oxidase]]		*[[Sarcosine oxidase\|Sarcosine oxidase]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacb0~~]]	+	[[Category: Bacillus sp. B-0618]]
	[[Category: Large Structures]]		[[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~~]]	+

OCA at 09:39, 21 July 2021

OCA — Wed, 21 Jul 2021 09:39:02 GMT

OCA at 11:16, 16 October 2019

OCA — Wed, 16 Oct 2019 11:16:36 GMT

←Older revision		Revision as of 11:16, 16 October 2019
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	==COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLTHIO]ACETATE==		==COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLTHIO]ACETATE==
-	<StructureSection load='1el9' size='340' side='right' caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>	+	<StructureSection load='1el9' size='340' side='right'caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1el9]] 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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EL9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1el9]] 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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EL9 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 1el9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1el9" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Sarcosine oxidase\|Sarcosine oxidase]]
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Bacb0]]		[[Category: Bacb0]]
		+	[[Category: Large Structures]]
	[[Category: Sarcosine oxidase]]		[[Category: Sarcosine oxidase]]
	[[Category: Chen, Z W]]		[[Category: Chen, Z W]]

OCA at 07:20, 20 December 2017

OCA — Wed, 20 Dec 2017 07:20:02 GMT

←Older revision		Revision as of 07:20, 20 December 2017
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		+
	==COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLTHIO]ACETATE==		==COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLTHIO]ACETATE==
	<StructureSection load='1el9' size='340' side='right' caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1el9' size='340' side='right' caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>
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	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1b3m\|1b3m]], [[1el5\|1el5]], [[1el7\|1el7]], [[1el8\|1el8]], [[1eli\|1eli]]</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]], [[1eli\|1eli]]</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='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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://pdbe.org/1el9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum]</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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://pdbe.org/1el9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1el9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	Check<jmol>		Check<jmol>
	<jmolCheckbox>		<jmolCheckbox>
-	<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/el/1el9_consurf.spt"</scriptWhenChecked>	+	<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/el/1el9_consurf.spt"</scriptWhenChecked>
	<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>		<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
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	</div>		</div>
	<div class="pdbe-citations 1el9" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 1el9" style="background-color:#fffaf0;"></div>
-
-	==See Also==
-	*[[Sarcosine oxidase\|Sarcosine oxidase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 04:41, 10 February 2016

OCA — Wed, 10 Feb 2016 04:41:49 GMT

←Older revision		Revision as of 04:41, 10 February 2016
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	<text>to colour the structure by Evolutionary Conservation</text>		<text>to colour the structure by Evolutionary Conservation</text>
	</jmolCheckbox>		</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/~~chain_selection~~.php?pdb_ID=~~2ata~~ ConSurf].	+	</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=1el9 ConSurf].
	<div style="clear:both"></div>		<div style="clear:both"></div>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">

OCA at 05:28, 11 September 2015

OCA — Fri, 11 Sep 2015 05:28:51 GMT

←Older revision		Revision as of 05:28, 11 September 2015
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	<StructureSection load='1el9' size='340' side='right' caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1el9' size='340' side='right' caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1el9]] is a 2 chain structure with sequence from [http://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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EL9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1el9]] 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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EL9 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=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>		</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=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1b3m\|1b3m]], [[1el5\|1el5]], [[1el7\|1el7]], [[1el8\|1el8]], [[1eli\|1eli]]</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]], [[1eli\|1eli]]</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='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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum]</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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://pdbe.org/1el9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
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	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>		From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
	</div>		</div>
		+	<div class="pdbe-citations 1el9" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==
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	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bacillus sp. b-0618~~]]	+	[[Category: Bacb0]]
	[[Category: Sarcosine oxidase]]		[[Category: Sarcosine oxidase]]
	[[Category: Chen, Z W]]		[[Category: Chen, Z W]]

OCA at 11:51, 25 December 2014

OCA — Thu, 25 Dec 2014 11:51:38 GMT

←Older revision		Revision as of 11:51, 25 December 2014
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	<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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum]</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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum]</span></td></tr>
	</table>		</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]
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]

OCA at 19:29, 22 December 2014

OCA — Mon, 22 Dec 2014 19:29:43 GMT

←Older revision		Revision as of 19:29, 22 December 2014
Line 3:		Line 3:
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[1el9]] is a 2 chain structure with sequence from [http://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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EL9 FirstGlance]. <br>		<table><tr><td colspan='2'>[[1el9]] is a 2 chain structure with sequence from [http://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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EL9 FirstGlance]. <br>
-	</td></tr><tr><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=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><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=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-	<tr><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='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><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1b3m\|1b3m]], [[1el5\|1el5]], [[1el7\|1el7]], [[1el8\|1el8]], [[1eli\|1eli]]</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]], [[1eli\|1eli]]</td></tr>
-	<tr><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='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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum]</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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum]</span></td></tr>
-	<table>	+	</table>
	== Evolutionary Conservation ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]
Line 36:		Line 36:
	[[Category: Bacillus sp. b-0618]]		[[Category: Bacillus sp. b-0618]]
	[[Category: Sarcosine oxidase]]		[[Category: Sarcosine oxidase]]
-	[[Category: Chen, Z W.]]	+	[[Category: Chen, Z W]]
-	[[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]]		[[Category: Flavoprotein]]
	[[Category: Oxidase]]		[[Category: Oxidase]]
	[[Category: Oxidoreductase]]		[[Category: Oxidoreductase]]

OCA at 11:29, 24 September 2014

OCA — Wed, 24 Sep 2014 11:29:54 GMT

←Older revision		Revision as of 11:29, 24 September 2014
Line 1:		Line 1:
-	[[~~Image:~~1el9.~~png~~\|~~left~~\|200px]]	+	==COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLTHIO]ACETATE==
		+	<StructureSection load='1el9' size='340' side='right' caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[1el9]] is a 2 chain structure with sequence from [http://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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1EL9 FirstGlance]. <br>
		+	</td></tr><tr><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=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene><br>
		+	<tr><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></td></tr>
		+	<tr><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1b3m\|1b3m]], [[1el5\|1el5]], [[1el7\|1el7]], [[1el8\|1el8]], [[1eli\|1eli]]</td></tr>
		+	<tr><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><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [http://www.ebi.ac.uk/pdbsum/1el9 PDBsum]</span></td></tr>
		+	<table>
		+	== 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/el/1el9_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/chain_selection.php?pdb_ID=2ata 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) < 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) < O < S < Se < 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)(+) > O > 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 < Se < 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 > O >> NH) is linearly correlated with the one-electron ionization potentials of the corresponding heterocyclic rings.

-	~~{{STRUCTURE_1el9\| PDB=1el9 \| SCENE= }}~~	+	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>

-	~~===COMPLEX OF MONOMERIC SARCOSINE OXIDASE WITH THE INHIBITOR [METHYLTHIO]ACETATE===~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>

-		+	==See Also==
-	==~~About this Structure~~==	+	*[[Sarcosine oxidase\|Sarcosine oxidase]]
-	[[~~1el9~~]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Bacillus_sp. Bacillus sp.]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1EL9 OCA].	+	== References ==
-		+	<references/>
-	==~~Reference~~==	+	__TOC__
-	<~~ref group="xtra">PMID:010913292<~~/~~ref~~><~~references group="xtra"~~/>	+	</StructureSection>
-	[[Category: Bacillus sp.]]	+	[[Category: Bacillus sp. b-0618]]
	[[Category: Sarcosine oxidase]]		[[Category: Sarcosine oxidase]]
	[[Category: Chen, Z W.]]		[[Category: Chen, Z W.]]

OCA: Protected "1el9" [edit=sysop:move=sysop]

OCA — Thu, 08 Nov 2012 14:41:31 GMT

Protected "1el9" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:41, 8 November 2012

←Older revision		Revision as of 09:39, 21 July 2021
Line 3:		Line 3:
	<StructureSection load='1el9' size='340' side='right'caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>		<StructureSection load='1el9' size='340' side='right'caption='[[1el9]], [[Resolution\|resolution]] 2.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[1el9]] 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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1EL9 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[1el9]] 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=1EL9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1EL9 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=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>	+	</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=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></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='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='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[1b3m\|1b3m]], [[1el5\|1el5]], [[1el7\|1el7]], [[1el8\|1el8]], [[1eli\|1eli]]</td></tr>	+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1b3m\|1b3m]], [[1el5\|1el5]], [[1el7\|1el7]], [[1el8\|1el8]], [[1eli\|1eli]]</div></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='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'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [~~http~~://pdbe.org/1el9 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/1el9 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=1el9 ProSAT]</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=1el9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1el9 OCA], [https://pdbe.org/1el9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1el9 RCSB], [https://www.ebi.ac.uk/pdbsum/1el9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1el9 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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 ==		== Evolutionary Conservation ==
	[[Image:Consurf_key_small.gif\|200px\|right]]		[[Image:Consurf_key_small.gif\|200px\|right]]