1ryi: Difference between revisions
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<StructureSection load='1ryi' size='340' side='right'caption='[[1ryi]], [[Resolution|resolution]] 1.80Å' scene=''> | <StructureSection load='1ryi' size='340' side='right'caption='[[1ryi]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1ryi]] is a 4 chain structure with sequence from [ | <table><tr><td colspan='2'>[[1ryi]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bacillus_subtilis Bacillus subtilis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RYI OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RYI FirstGlance]. <br> | ||
</td></tr><tr id=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</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=GOA:GLYCOLIC+ACID'>GOA</scene></td></tr> | |||
<tr id=' | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ryi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryi OCA], [https://pdbe.org/1ryi PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ryi RCSB], [https://www.ebi.ac.uk/pdbsum/1ryi PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ryi ProSAT]</span></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == Function == | ||
[ | [https://www.uniprot.org/uniprot/GLYOX_BACSU GLYOX_BACSU] Catalyzes the FAD-dependent oxidative deamination of various amines and D-amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Oxidizes sarcosine (N-methylglycine), N-ethylglycine and glycine (PubMed:9827558, PubMed:11744710, PubMed:19864430). Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine) (PubMed:19864430). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine (PubMed:9827558, PubMed:11744710). Does not act on L-amino acids and other D-amino acids (PubMed:9827558). Is essential for thiamine biosynthesis since the oxidation of glycine catalyzed by ThiO generates the glycine imine intermediate (dehydroglycine) required for the biosynthesis of the thiazole ring of thiamine pyrophosphate (PubMed:12627963).<ref>PMID:11744710</ref> <ref>PMID:12627963</ref> <ref>PMID:19864430</ref> <ref>PMID:9827558</ref> | ||
== Evolutionary Conservation == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Bacillus | [[Category: Bacillus subtilis]] | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: Andriolo | [[Category: Andriolo G]] | ||
[[Category: Diederichs | [[Category: Diederichs K]] | ||
[[Category: Moertl | [[Category: Moertl M]] | ||
[[Category: Molla | [[Category: Molla G]] | ||
[[Category: Motteran | [[Category: Motteran L]] | ||
[[Category: Pilone | [[Category: Pilone MS]] | ||
[[Category: Pollegioni | [[Category: Pollegioni L]] | ||
[[Category: Welte | [[Category: Welte W]] | ||
Latest revision as of 11:04, 15 November 2023
STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATESTRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE
Structural highlights
FunctionGLYOX_BACSU Catalyzes the FAD-dependent oxidative deamination of various amines and D-amino acids to yield the corresponding alpha-keto acids, ammonia/amine, and hydrogen peroxide. Oxidizes sarcosine (N-methylglycine), N-ethylglycine and glycine (PubMed:9827558, PubMed:11744710, PubMed:19864430). Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine) (PubMed:19864430). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine (PubMed:9827558, PubMed:11744710). Does not act on L-amino acids and other D-amino acids (PubMed:9827558). Is essential for thiamine biosynthesis since the oxidation of glycine catalyzed by ThiO generates the glycine imine intermediate (dehydroglycine) required for the biosynthesis of the thiazole ring of thiamine pyrophosphate (PubMed:12627963).[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 PubMedStructure-function relationships of the flavoprotein glycine oxidase (GO), which was recently proposed as the first enzyme in the biosynthesis of thiamine in Bacillus subtilis, has been investigated by a combination of structural and functional studies. The structure of the GO-glycolate complex was determined at 1.8 A, a resolution at which a sketch of the residues involved in FAD binding and in substrate interaction can be depicted. GO can be considered a member of the "amine oxidase" class of flavoproteins, such as d-amino acid oxidase and monomeric sarcosine oxidase. With the obtained model of GO the monomer-monomer interactions can be analyzed in detail, thus explaining the structural basis of the stable tetrameric oligomerization state of GO, which is unique for the GR(2) subfamily of flavooxidases. On the other hand, the three-dimensional structure of GO and the functional experiments do not provide the functional significance of such an oligomerization state; GO does not show an allosteric behavior. The results do not clarify the metabolic role of this enzyme in B. subtilis; the broad substrate specificity of GO cannot be correlated with the inferred function in thiamine biosynthesis, and the structure does not show how GO could interact with ThiS, the following enzyme in thiamine biosynthesis. However, they do let a general catabolic role of this enzyme on primary or secondary amines to be excluded because the expression of GO is not inducible by glycine, sarcosine, or d-alanine as carbon or nitrogen sources. Structure-function correlation in glycine oxidase from Bacillus subtilis.,Mortl M, Diederichs K, Welte W, Molla G, Motteran L, Andriolo G, Pilone MS, Pollegioni L J Biol Chem. 2004 Jul 9;279(28):29718-27. Epub 2004 Apr 22. PMID:15105420[5] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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