1ng4

From Proteopedia

(Difference between revisions)

Revision as of 08:50, 2 December 2020

Structure of ThiO (glycine oxidase) from Bacillus subtilis

Structural highlights

1ng4 is a 2 chain structure with sequence from "bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, ,
Related:	1ng3
Gene:	GOXB ("Bacillus globigii" Migula 1900)
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

[GLOX_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. Can also oxidize the herbicide glyphosate (N-phosphonomethylglycine). Displays lower activities on D-alanine, D-valine, D-proline and D-methionine. Does not act on L-amino acids and other D-amino acids. 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.^[1] ^[2]

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

The thiO gene of Bacillus subtilis encodes an FAD-dependent glycine oxidase. This enzyme is a homotetramer with a monomer molecular mass of 42 kDa. In this paper, we demonstrate that ThiO is required for the biosynthesis of the thiazole moiety of thiamin pyrophosphate and describe the structure of the enzyme with N-acetylglycine bound at the active site. The closest structural relatives of ThiO are sarcosine oxidase and d-amino acid oxidase. The ThiO structure, as well as the observation that N-cyclopropylglycine is a good substrate, supports a hydride transfer mechanism for the enzyme. A mechanistic proposal for the role of ThiO in thiazole biosynthesis is also described.

Structural and mechanistic studies on ThiO, a glycine oxidase essential for thiamin biosynthesis in Bacillus subtilis.,Settembre EC, Dorrestein PC, Park JH, Augustine AM, Begley TP, Ealick SE Biochemistry. 2003 Mar 18;42(10):2971-81. PMID:12627963^[3]

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

References

↑ 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
↑ 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
↑ 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

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/1ng4"

@@ Line 1: / Line 1: @@
 ==Structure of ThiO (glycine oxidase) from Bacillus subtilis==
-<StructureSection load='1ng4' size='340' side='right' caption='[[1ng4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='1ng4' size='340' side='right'caption='[[1ng4]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1ng4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NG4 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1NG4 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1ng4]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/"bacillus_globigii"_migula_1900 "bacillus globigii" migula 1900]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NG4 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=1NG4 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=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
+</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=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1ng3|1ng3]]</td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat"><div style='overflow: auto; max-height: 3em;'>[[1ng3|1ng3]]</div></td></tr>
 <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">GOXB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1423 "Bacillus globigii" Migula 1900])</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=1ng4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ng4 OCA], [http://pdbe.org/1ng4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ng4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ng4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ng4 ProSAT]</span></td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=1ng4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ng4 OCA], [http://pdbe.org/1ng4 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1ng4 RCSB], [http://www.ebi.ac.uk/pdbsum/1ng4 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1ng4 ProSAT]</span></td></tr>
 </table>
 == Function ==
@@ Line 15: / Line 15: @@
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ng/1ng4_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/ng/1ng4_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 35: / Line 35: @@
 </StructureSection>
 [[Category: Bacillus globigii migula 1900]]
+[[Category: Large Structures]]
 [[Category: Augustine, A]]
 [[Category: Begley, T P]]

1ng4

From Proteopedia

Revision as of 08:50, 2 December 2020

Structure of ThiO (glycine oxidase) from Bacillus subtilis

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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