4e2s: Difference between revisions

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== Structural highlights ==
== Structural highlights ==
<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>
<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" id="ligandDat"><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='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='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'>[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>
</table>
</table>
== Function ==
== 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>
[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;">
== 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&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/>

Latest revision as of 11:49, 20 March 2024

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

4e2s is a 16 chain structure with sequence from Arabidopsis thaliana. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 2.59Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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]

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 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

4e2s, resolution 2.59Å

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