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5hp8

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Revision as of 08:26, 27 May 2020

Crystal structures of RidA in complex with pyruvate

Structural highlights

5hp8 is a 3 chain structure with sequence from Arath. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:
Related:	5hp7
Gene:	RIDA, At3g20390, MQC12.15 (ARATH)
Activity:	2-iminobutanoate/2-iminopropanoate deaminase, with EC number 3.5.99.10
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5hp8"

@@ Line 1: / Line 1: @@
 ==Crystal structures of RidA in complex with pyruvate==
-<StructureSection load='5hp8' size='340' side='right' caption='[[5hp8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
+<StructureSection load='5hp8' size='340' side='right'caption='[[5hp8]], [[Resolution|resolution]] 2.30&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5hp8]] is a 3 chain structure. 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://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5HP8 FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=PYR:PYRUVIC+ACID'>PYR</scene></td></tr>
+</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5hp7|5hp7]]</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='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://oca.weizmann.ac.il/oca-docs/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>
+<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>
 == Function ==
@@ Line 25: / Line 26: @@
 </StructureSection>
 [[Category: 2-iminobutanoate/2-iminopropanoate deaminase]]
+[[Category: Arath]]
+[[Category: Large Structures]]
 [[Category: Liu, X]]
 [[Category: Xie, W]]

5hp8

From Proteopedia

Revision as of 08:26, 27 May 2020

Crystal structures of RidA in complex with pyruvate

Structural highlights

Function

Publication Abstract from PubMed

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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