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| | <StructureSection load='5hp8' size='340' side='right'caption='[[5hp8]], [[Resolution|resolution]] 2.30Å' scene=''> | | <StructureSection load='5hp8' size='340' side='right'caption='[[5hp8]], [[Resolution|resolution]] 2.30Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5hp8]] is a 3 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=5HP8 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5HP8 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5hp8]] is a 3 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=5HP8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5HP8 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</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]] 2.3Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5hp7|5hp7]]</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">RIDA, At3g20390, MQC12.15 ([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=5hp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp8 OCA], [https://pdbe.org/5hp8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5hp8 RCSB], [https://www.ebi.ac.uk/pdbsum/5hp8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp8 ProSAT]</span></td></tr> |
| - | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/2-iminobutanoate/2-iminopropanoate_deaminase 2-iminobutanoate/2-iminopropanoate deaminase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.99.10 3.5.99.10] </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=5hp8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5hp8 OCA], [http://pdbe.org/5hp8 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5hp8 RCSB], [http://www.ebi.ac.uk/pdbsum/5hp8 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5hp8 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/RIDA_ARATH RIDA_ARATH]] Hydrolyzes the Ser-derived enamine/imine product of Thr dehydratase, protecting the plastidial branched-chain aminotransferase BCAT3 (AC Q9M401) from inactivation. Involved in Ile biosynthesis.<ref>PMID:25070638</ref> | + | [https://www.uniprot.org/uniprot/RIDA_ARATH RIDA_ARATH] Hydrolyzes the Ser-derived enamine/imine product of Thr dehydratase, protecting the plastidial branched-chain aminotransferase BCAT3 (AC Q9M401) from inactivation. Involved in Ile biosynthesis.<ref>PMID:25070638</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: 2-iminobutanoate/2-iminopropanoate deaminase]] | + | [[Category: Arabidopsis thaliana]] |
| - | [[Category: Arath]]
| + | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Liu, X]] | + | [[Category: Liu X]] |
| - | [[Category: Xie, W]] | + | [[Category: Xie W]] |
| - | [[Category: Deamination]]
| + | |
| - | [[Category: Enamine/imine]]
| + | |
| - | [[Category: Hydrolase]]
| + | |
| - | [[Category: Rida]]
| + | |
| Structural highlights
Function
RIDA_ARATH Hydrolyzes the Ser-derived enamine/imine product of Thr dehydratase, protecting the plastidial branched-chain aminotransferase BCAT3 (AC Q9M401) from inactivation. Involved in Ile biosynthesis.[1]
Publication Abstract from PubMed
The YjgF/YER057c/UK114 family proteins are highly conserved across all three domains of life, and most of them currently have no clearly defined biological roles. In vitro, these proteins were found to hydrolyze the enamine/imine intermediates generated from serine or threonine, and were renamed Reactive Intermediate Deaminase A (RidA). RidA was recently discovered in Arabidopsis thaliana, and by deaminating the toxic enamine/imine intermediates, it prevents the inactivation of many functionally important pyridoxal 5'-phosphate (PLP)-containing enzymes in plants such as branched-chain aminotransferase BCAT (IlvE). In this study, we determined the crystal structure of Arabidopsis thaliana RidA in the apo form, as well as RidA complexed with the ligand pyruvate. RidA forms the trimeric, barrel-like quaternary structure and inter-subunit cavities, and resembles most RidA family members. Each pyruvate molecule binds to the interface between two subunits, and the recognition of pyruvate is achieved by the interactions with R165 and T167. From sequence alignment and structural superposition, we identified a series of key residues responsible for the trimer assembly, whose importance was confirmed by enzymatic assays. This study provides structural insight into RidA functions in plants.
Crystal structures of RidA, an important enzyme for the prevention of toxic side products.,Liu X, Zeng J, Chen X, Xie W Sci Rep. 2016 Jul 26;6:30494. doi: 10.1038/srep30494. PMID:27458092[2]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Niehaus TD, Nguyen TN, Gidda SK, ElBadawi-Sidhu M, Lambrecht JA, McCarty DR, Downs DM, Cooper AJ, Fiehn O, Mullen RT, Hanson AD. Arabidopsis and maize RidA proteins preempt reactive enamine/imine damage to branched-chain amino acid biosynthesis in plastids. Plant Cell. 2014 Jul;26(7):3010-22. doi: 10.1105/tpc.114.126854. Epub 2014 Jul, 28. PMID:25070638 doi:http://dx.doi.org/10.1105/tpc.114.126854
- ↑ Liu X, Zeng J, Chen X, Xie W. Crystal structures of RidA, an important enzyme for the prevention of toxic side products. Sci Rep. 2016 Jul 26;6:30494. doi: 10.1038/srep30494. PMID:27458092 doi:http://dx.doi.org/10.1038/srep30494
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