1pj7

From Proteopedia

(Difference between revisions)

Current revision

Structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folinic acid

Structural highlights

1pj7 is a 1 chain structure with sequence from Arthrobacter globiformis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.1Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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.^[1] ^[2] ^[3] ^[4]

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 PubMed

Here we report crystal structures of dimethylglycine oxidase (DMGO) from the bacterium Arthrobacter globiformis, a bifunctional enzyme that catalyzes the oxidation of N,N-dimethyl glycine and the formation of 5,10-methylene tetrahydrofolate. The N-terminal region binds FAD covalently and oxidizes dimethylglycine to a labile iminium intermediate. The C-terminal region binds tetrahydrofolate, comprises three domains arranged in a ring-like structure and is related to the T-protein of the glycine cleavage system. The complex with folinic acid indicates that this enzyme selectively activates the N10 amino group for initial attack on the substrate. Dead-end reactions with oxidized folate are avoided by the strict stereochemical constraints imposed by the folate-binding funnel. The active sites in DMGO are approximately 40 A apart, connected by a large irregular internal cavity. The tetrahydrofolate-binding funnel serves as a transient entry-exit port, and access to the internal cavity is controlled kinetically by tetrahydrofolate binding. The internal cavity enables sequestration of the reactive iminium intermediate prior to reaction with tetrahydrofolate and avoids formation of toxic formaldehyde. This mode of channelling in DMGO is distinct from other channelling mechanisms.

Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase.,Leys D, Basran J, Scrutton NS EMBO J. 2003 Aug 15;22(16):4038-48. PMID:12912903^[5]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Meskys R, Harris RJ, Casaite V, Basran J, Scrutton NS. Organization of the genes involved in dimethylglycine and sarcosine degradation in Arthrobacter spp.: implications for glycine betaine catabolism. Eur J Biochem. 2001 Jun;268(12):3390-8. PMID:11422368 doi:10.1046/j.1432-1327.2001.02239.x
↑ Basran J, Bhanji N, Basran A, Nietlispach D, Mistry S, Meskys R, Scrutton NS. Mechanistic aspects of the covalent flavoprotein dimethylglycine oxidase of Arthrobacter globiformis studied by stopped-flow spectrophotometry. Biochemistry. 2002 Apr 9;41(14):4733-43. PMID:11926836 doi:10.1021/bi025519h
↑ Leys D, Basran J, Scrutton NS. Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase. EMBO J. 2003 Aug 15;22(16):4038-48. PMID:12912903 doi:http://dx.doi.org/10.1093/emboj/cdg395
↑ Tralau T, Lafite P, Levy C, Combe JP, Scrutton NS, Leys D. An internal reaction chamber in dimethylglycine oxidase provides efficient protection from exposure to toxic formaldehyde. J Biol Chem. 2009 Jun 26;284(26):17826-34. Epub 2009 Apr 15. PMID:19369258 doi:10.1074/jbc.M109.006262
↑ Leys D, Basran J, Scrutton NS. Channelling and formation of 'active' formaldehyde in dimethylglycine oxidase. EMBO J. 2003 Aug 15;22(16):4038-48. PMID:12912903 doi:http://dx.doi.org/10.1093/emboj/cdg395

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1pj7"

Categories: Arthrobacter globiformis | Large Structures | Basran J | Leys D | Scrutton NS

@@ Line 3: / Line 3: @@
 <StructureSection load='1pj7' size='340' side='right'caption='[[1pj7]], [[Resolution|resolution]] 2.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1pj7]] is a 1 chain structure with sequence from [https://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=1PJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PJ7 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1pj7]] 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=1PJ7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1PJ7 FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FFO:N-[4-({[(6S)-2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC+ACID'>FFO</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]] 2.1&#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;'>[[1pj5|1pj5]], [[1pj6|1pj6]]</div></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=FFO:N-[4-({[(6S)-2-AMINO-5-FORMYL-4-OXO-3,4,5,6,7,8-HEXAHYDROPTERIDIN-6-YL]METHYL}AMINO)BENZOYL]-L-GLUTAMIC+ACID'>FFO</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'>[https://en.wikipedia.org/wiki/Dimethylglycine_oxidase Dimethylglycine oxidase], with EC number [https://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=1pj7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1pj7 OCA], [https://pdbe.org/1pj7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1pj7 RCSB], [https://www.ebi.ac.uk/pdbsum/1pj7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1pj7 ProSAT]</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]]
@@ Line 14: / Line 15: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/pj/1pj7_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 32: / Line 33: @@
 __TOC__
 </StructureSection>
-[[Category: Dimethylglycine oxidase]]
+[[Category: Arthrobacter globiformis]]
 [[Category: Large Structures]]
-[[Category: Basran, J]]
+[[Category: Basran J]]
-[[Category: Leys, D]]
+[[Category: Leys D]]
-[[Category: Scrutton, N S]]
+[[Category: Scrutton NS]]
-[[Category: Amine oxidation]]
-[[Category: Channelling]]
-[[Category: Fad binding]]
-[[Category: Folate binding]]
-[[Category: Folinic acid]]
-[[Category: Oxidoreductase]]

1pj7

From Proteopedia

Current revision

Structure of dimethylglycine oxidase of Arthrobacter globiformis in complex with folinic acid

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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