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==Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate== | ==Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate== | ||
<StructureSection load='3ad7' size='340' side='right' caption='[[3ad7]], [[Resolution|resolution]] 2.20Å' scene=''> | <StructureSection load='3ad7' size='340' side='right' caption='[[3ad7]], [[Resolution|resolution]] 2.20Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3ad7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/ | <table><tr><td colspan='2'>[[3ad7]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Corynebacterium_u-96 Corynebacterium u-96]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AD7 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3AD7 FirstGlance]. <br> | ||
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FMN:FLAVIN+MONONUCLEOTIDE'>FMN</scene>, <scene name='pdbligand=MTG:[METHYLTHIO]ACETATE'>MTG</scene>, <scene name='pdbligand=NAD:NICOTINAMIDE-ADENINE-DINUCLEOTIDE'>NAD</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></td></tr> | ||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x31|1x31]], [[1vrq|1vrq]], [[3ad8|3ad8]], [[3ad9|3ad9]], [[3ada|3ada]]</td></tr> | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1x31|1x31]], [[1vrq|1vrq]], [[3ad8|3ad8]], [[3ad9|3ad9]], [[3ada|3ada]]</td></tr> | ||
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">soxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31944 Corynebacterium | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">soxA ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31944 Corynebacterium U-96]), soxB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31944 Corynebacterium U-96]), soxG ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31944 Corynebacterium U-96]), soxD ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=31944 Corynebacterium U-96])</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=3ad7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ad7 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3ad7 RCSB], [http://www.ebi.ac.uk/pdbsum/3ad7 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=3ad7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ad7 OCA], [http://pdbe.org/3ad7 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3ad7 RCSB], [http://www.ebi.ac.uk/pdbsum/3ad7 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3ad7 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
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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/ | </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=3ad7 ConSurf]. | ||
<div style="clear:both"></div> | <div style="clear:both"></div> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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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 3ad7" style="background-color:#fffaf0;"></div> | |||
==See Also== | ==See Also== | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Corynebacterium | [[Category: Corynebacterium u-96]] | ||
[[Category: Sarcosine oxidase]] | [[Category: Sarcosine oxidase]] | ||
[[Category: Ida, K]] | [[Category: Ida, K]] | ||
Revision as of 11:57, 11 August 2016
Heterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetateHeterotetrameric Sarcosine Oxidase from Corynebacterium sp. U-96 in complex with methylthio acetate
Structural highlights
Evolutionary Conservation Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedWe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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