1ryi

From Proteopedia

(Difference between revisions)

Current revision

STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE

Structural highlights

1ryi is a 4 chain structure with sequence from Bacillus subtilis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.8Å
Ligands:	,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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).^[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

Structure-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

↑ Job V, Marcone GL, Pilone MS, Pollegioni L. Glycine oxidase from Bacillus subtilis. Characterization of a new flavoprotein. J Biol Chem. 2002 Mar 1;277(9):6985-93. PMID:11744710 doi:10.1074/jbc.M111095200
↑ Settembre EC, Dorrestein PC, Park JH, Augustine AM, Begley TP, Ealick SE. Structural and mechanistic studies on ThiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis. Biochemistry. 2003 Mar 18;42(10):2971-81. PMID:12627963 doi:10.1021/bi026916v
↑ Pedotti M, Rosini E, Molla G, Moschetti T, Savino C, Vallone B, Pollegioni L. Glyphosate resistance by engineering the flavoenzyme glycine oxidase. J Biol Chem. 2009 Dec 25;284(52):36415-23. Epub 2009 Oct 28. PMID:19864430 doi:http://dx.doi.org/10.1074/jbc.M109.051631
↑ Nishiya Y, Imanaka T. Purification and characterization of a novel glycine oxidase from Bacillus subtilis. FEBS Lett. 1998 Nov 6;438(3):263-6. PMID:9827558
↑ Mortl M, Diederichs K, Welte W, Molla G, Motteran L, Andriolo G, Pilone MS, Pollegioni L. Structure-function correlation in glycine oxidase from Bacillus subtilis. J Biol Chem. 2004 Jul 9;279(28):29718-27. Epub 2004 Apr 22. PMID:15105420 doi:10.1074/jbc.M401224200

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/1ryi"

@@ Line 1: / Line 1: @@
 ==STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE==
-<StructureSection load='1ryi' size='340' side='right' caption='[[1ryi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+<StructureSection load='1ryi' size='340' side='right'caption='[[1ryi]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ryi]] is a 4 chain structure with sequence from [http://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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1RYI FirstGlance]. <br>
+<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><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=FAD:FLAVIN-ADENINE+DINUCLEOTIDE'>FAD</scene>, <scene name='pdbligand=GOA:GLYCOLIC+ACID'>GOA</scene><br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8&#8491;</td></tr>
-<tr><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ng3|1ng3]], [[1ng4|1ng4]]</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><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GOXB, BSU11670 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 Bacillus subtilis])</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=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><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glycine_oxidase Glycine oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.3.19 1.4.3.19] </span></td></tr>
+</table>
-<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=1ryi FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ryi OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1ryi RCSB], [http://www.ebi.ac.uk/pdbsum/1ryi PDBsum]</span></td></tr>
+== Function ==
-<table>
+[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 ==
 [[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/ry/1ryi_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ry/1ryi_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].
+</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=1ryi ConSurf].
 <div style="clear:both"></div>
 <div style="background-color:#fffaf0;">
@@ Line 27: / Line 28: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 1ryi" style="background-color:#fffaf0;"></div>
 == References ==
 <references/>
@@ Line 32: / Line 34: @@
 </StructureSection>
 [[Category: Bacillus subtilis]]
-[[Category: Glycine oxidase]]
+[[Category: Large Structures]]
-[[Category: Andriolo, G.]]
+[[Category: Andriolo G]]
-[[Category: Diederichs, K.]]
+[[Category: Diederichs K]]
-[[Category: Moertl, M.]]
+[[Category: Moertl M]]
-[[Category: Molla, G.]]
+[[Category: Molla G]]
-[[Category: Motteran, L.]]
+[[Category: Motteran L]]
-[[Category: Pilone, M S.]]
+[[Category: Pilone MS]]
-[[Category: Pollegioni, L.]]
+[[Category: Pollegioni L]]
-[[Category: Welte, W.]]
+[[Category: Welte W]]
-[[Category: Flavoprotein]]
-[[Category: Oxidase]]
-[[Category: Oxidoreductase]]
-[[Category: Protein-inhibitor complex]]

1ryi

From Proteopedia

Current revision

STRUCTURE OF GLYCINE OXIDASE WITH BOUND INHIBITOR GLYCOLATE

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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