4e2s: Difference between revisions
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==Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-Ureidoglycine== | |||
<StructureSection load='4e2s' size='340' side='right' caption='[[4e2s]], [[Resolution|resolution]] 2.59Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[4e2s]] is a 16 chain structure with sequence from [http://en.wikipedia.org/wiki/Arabidopsis_thaliana Arabidopsis thaliana]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4E2S OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4E2S 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>, <scene name='pdbligand=UGY:(2S)-AMINO(CARBAMOYLAMINO)ETHANOIC+ACID'>UGY</scene></td></tr> | |||
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4e2q|4e2q]]</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 Arabidopsis thaliana])</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=4e2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2s OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4e2s RCSB], [http://www.ebi.ac.uk/pdbsum/4e2s PDBsum]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== 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<ref>PMID:22493446</ref> | |||
== | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | ||
</div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Arabidopsis thaliana]] | [[Category: Arabidopsis thaliana]] | ||
[[Category: Rhee, S | [[Category: Rhee, S]] | ||
[[Category: Shin, I | [[Category: Shin, I]] | ||
[[Category: Bi-cupin]] | [[Category: Bi-cupin]] | ||
[[Category: Endoplasmic reticulumn]] | [[Category: Endoplasmic reticulumn]] | ||
[[Category: Hydrolase]] | [[Category: Hydrolase]] | ||
[[Category: Manganese binding]] | [[Category: Manganese binding]] | ||
Revision as of 15:31, 5 January 2015
Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-UreidoglycineCrystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-Ureidoglycine
Structural highlights
Publication Abstract from PubMedThe 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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