This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


4e2s

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:49, 20 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
==Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-Ureidoglycine==
==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]] 2.59&Aring;' scene=''>
+
<StructureSection load='4e2s' size='340' side='right'caption='[[4e2s]], [[Resolution|resolution]] 2.59&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[4e2s]] 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=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>
+
<table><tr><td colspan='2'>[[4e2s]] 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=4E2S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/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>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.59&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4e2q|4e2q]]</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>, <scene name='pdbligand=UGY:(2S)-AMINO(CARBAMOYLAMINO)ETHANOIC+ACID'>UGY</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=4e2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2s OCA], [https://pdbe.org/4e2s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4e2s RCSB], [https://www.ebi.ac.uk/pdbsum/4e2s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2s 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=4e2s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4e2s OCA], [http://pdbe.org/4e2s PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4e2s RCSB], [http://www.ebi.ac.uk/pdbsum/4e2s PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4e2s ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[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>
-
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&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 4e2s" style="background-color:#fffaf0;"></div>
+
== References ==
== References ==
<references/>
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Arath]]
+
[[Category: Arabidopsis thaliana]]
-
[[Category: Rhee, S]]
+
[[Category: Large Structures]]
-
[[Category: Shin, I]]
+
[[Category: Rhee S]]
-
[[Category: Bi-cupin]]
+
[[Category: Shin I]]
-
[[Category: Endoplasmic reticulumn]]
+
-
[[Category: Hydrolase]]
+
-
[[Category: Manganese binding]]
+

Current revision

Crystal structure of (S)-Ureidoglycine Aminohydrolase from Arabidopsis thaliana in complex with its substrate, (S)-Ureidoglycine

PDB ID 4e2s

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/4e2s"
Personal tools