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| | ==Crystal Structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana== | | ==Crystal Structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana== |
| - | <StructureSection load='4e2q' size='340' side='right' caption='[[4e2q]], [[Resolution|resolution]] 2.50Å' scene=''> | + | <StructureSection load='4e2q' size='340' side='right'caption='[[4e2q]], [[Resolution|resolution]] 2.50Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[4e2q]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Arath Arath]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E2Q OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2Q FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[4e2q]] is a 16 chain structure with sequence from [https://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E2Q OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4E2Q FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> | + | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ylbA, UGLYAH, At4g17050, AT4G17050 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=3702 ARATH])</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=4e2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2q OCA], [https://pdbe.org/4e2q PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e2q RCSB], [https://www.ebi.ac.uk/pdbsum/4e2q PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2q 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=4e2q FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2q OCA], [http://pdbe.org/4e2q PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e2q RCSB], [http://www.ebi.ac.uk/pdbsum/4e2q PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2q ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | + | == Function == |
| | + | [[https://www.uniprot.org/uniprot/UGHY_ARATH UGHY_ARATH]] Involved in the catabolism of purine nucleotides. Can use (S)-2-ureidoglycine as substrate, but not allantoate. The sequential activity of AAH, UGLYAH and UAH allows a complete purine breakdown without the intermediate generation of urea.<ref>PMID:19935661</ref> <ref>PMID:20038185</ref> <ref>PMID:22493446</ref> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Arath]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Rhee, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Shin, I]] | + | [[Category: Rhee S]] |
| - | [[Category: Aminohydrolase]] | + | [[Category: Shin I]] |
| - | [[Category: Bi-cupin]]
| + | |
| - | [[Category: Endoplasmic reticulum]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Manganese binding]]
| + | |
| Structural highlights
Function
[UGHY_ARATH] Involved in the catabolism of purine nucleotides. Can use (S)-2-ureidoglycine as substrate, but not allantoate. The sequential activity of AAH, UGLYAH and UAH allows a complete purine breakdown without the intermediate generation of urea.[1] [2] [3]
Publication Abstract from PubMed
The ureide pathway has recently been identified as the metabolic route of purine catabolism in plants and some bacteria. In this pathway, uric acid, which is a major product of the early stage of purine catabolism, is degraded into glyoxylate and ammonia via stepwise reactions of seven different enzymes. Therefore, the pathway has a possible physiological role in mobilization of purine ring nitrogen for further assimilation. (S)-Ureidoglycine aminohydrolase enzyme converts (S)-ureidoglycine into (S)-ureidoglycolate and ammonia, providing the final substrate to the pathway. Here, we report a structural and functional analysis of this enzyme from Arabidopsis thaliana (AtUGlyAH). The crystal structure of AtUGlyAH in the ligand-free form shows a monomer structure in the bicupin fold of the beta-barrel and an octameric functional unit as well as a Mn(2+) ion binding site. The structure of AtUGlyAH in complex with (S)-ureidoglycine revealed that the Mn(2+) ion acts as a molecular anchor to bind (S)-ureidoglycine, and its binding mode dictates the enantioselectivity of the reaction. Further kinetic analysis characterized the functional roles of the active site residues, including the Mn(2+) ion binding site and residues in the vicinity of (S)-ureidoglycine. These analyses provide molecular insights into the structure of the enzyme and its possible catalytic mechanism.
Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana.,Shin I, Percudani R, Rhee S J Biol Chem. 2012 May 25;287(22):18796-805. Epub 2012 Apr 5. PMID:22493446[4]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Werner AK, Romeis T, Witte CP. Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat Chem Biol. 2010 Jan;6(1):19-21. Epub 2009 Nov 22. PMID:19935661 doi:http://dx.doi.org/nchembio.265
- ↑ Serventi F, Ramazzina I, Lamberto I, Puggioni V, Gatti R, Percudani R. Chemical basis of nitrogen recovery through the ureide pathway: formation and hydrolysis of S-ureidoglycine in plants and bacteria. ACS Chem Biol. 2010 Feb 19;5(2):203-14. doi: 10.1021/cb900248n. PMID:20038185 doi:http://dx.doi.org/10.1021/cb900248n
- ↑ Shin I, Percudani R, Rhee S. Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana. J Biol Chem. 2012 May 25;287(22):18796-805. Epub 2012 Apr 5. PMID:22493446 doi:10.1074/jbc.M111.331819
- ↑ Shin I, Percudani R, Rhee S. Structural and functional insights into (S)-ureidoglycine aminohydrolase, key enzyme of purine catabolism in Arabidopsis thaliana. J Biol Chem. 2012 May 25;287(22):18796-805. Epub 2012 Apr 5. PMID:22493446 doi:10.1074/jbc.M111.331819
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