1pj5: Difference between revisions

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 ==Crystal structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with acetate==
-<StructureSection load='1pj5' size='340' side='right' caption='[[1pj5]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
+<StructureSection load='1pj5' size='340' side='right'caption='[[1pj5]], [[Resolution|resolution]] 1.61&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pj5]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"achromobacter_globiformis"_(conn_1928)_bergey_et_al._1930 "achromobacter globiformis" (conn 1928) bergey et al. 1930]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PJ5 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1PJ5 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pj5]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Arthrobacter_globiformis Arthrobacter globiformis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1PJ5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PJ5 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.61&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1pj6|1pj6]], [[1pj7|1pj7]]</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Dimethylglycine_oxidase Dimethylglycine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.5.3.10 1.5.3.10] </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=1pj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pj5 OCA], [https://pdbe.org/1pj5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pj5 RCSB], [https://www.ebi.ac.uk/pdbsum/1pj5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pj5 ProSAT]</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=1pj5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pj5 OCA], [http://pdbe.org/1pj5 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1pj5 RCSB], [http://www.ebi.ac.uk/pdbsum/1pj5 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/DMGO_ARTGO DMGO_ARTGO] Catalyzes the oxidative demethylation of N,N-dimethylglycine to yield sarcosine, formaldehyde and hydrogen peroxide. The oxidation of dimethylglycine is coupled to the synthesis of 5,10-methylenetetrahydrofolate through an unusual substrate channeling mechanism. This channeling occurs by nonbiased diffusion of the iminium intermediate through a large solvent cavity connecting active site 1 (N-terminus) and active site 2 (C-terminus). The synthesis of 5,10-methylenetetrahydrofolate (at active site 2) prevents the accumulation of formaldehyde, formed by hydrolysis of the iminium intermediate product (at active site 1). Does not oxidize sarcosine.<ref>PMID:11422368</ref> <ref>PMID:11926836</ref> <ref>PMID:12912903</ref> <ref>PMID:19369258</ref>
 == 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/pj/1pj5_consurf.spt"</scriptWhenChecked>
+     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pj/1pj5_consurf.spt"</scriptWhenChecked>
-     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
+     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
      <text>to colour the structure by Evolutionary Conservation</text>
    </jmolCheckbox>
@@ Line 31: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Dimethylglycine oxidase]]
+[[Category: Arthrobacter globiformis]]
-[[Category: Basran, J]]
+[[Category: Large Structures]]
-[[Category: Leys, D]]
+[[Category: Basran J]]
-[[Category: Scrutton, N S]]
+[[Category: Leys D]]
-[[Category: Amine oxidase]]
+[[Category: Scrutton NS]]
-[[Category: Channelling]]
-[[Category: Fad binding]]
-[[Category: Folate binding]]
-[[Category: Oxidoreductase]]