6ils: Difference between revisions
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The entry | ==Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP== | ||
<StructureSection load='6ils' size='340' side='right'caption='[[6ils]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[6ils]] is a 2 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=6ILS OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6ILS FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.8Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ATP:ADENOSINE-5-TRIPHOSPHATE'>ATP</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=RIB:RIBOSE'>RIB</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=6ils FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ils OCA], [https://pdbe.org/6ils PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ils RCSB], [https://www.ebi.ac.uk/pdbsum/6ils PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ils ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/RBSK_ARATH RBSK_ARATH] Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway (By similarity) (PubMed:27601466). Can also use xylose and fructose as carbohydrate substrates with a low efficiency (PubMed:27601466). Can use GTP, and, to a lower extent, CTP and UTP as alternative phosphoryl donors (PubMed:27601466).[HAMAP-Rule:MF_03215]<ref>PMID:27601466</ref> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Nitrogen remobilization is a key issue in plants. Recent studies in Arabidopsis thaliana have revealed that nucleoside catabolism supplies xanthine, a nitrogen-rich compound, to the purine ring catabolic pathway, which liberates ammonia from xanthine for reassimilation into amino acids. Similarly, pyrimidine nuclosides are degraded and the pyrimidine bases are fully catabolized. During nucleoside hydrolysis, ribose is released, and ATP-dependent ribokinase (RBSK) phosphorylates ribose to ribose-5'-phosphate to allow its entry into central metabolism recycling the sugar carbons from nucleosides. In this study, we report the crystal structure of RBSK from Arapidopsis thaliana (AtRBSK) in three different ligation states: an unliganded state, a ternary complex with ribose and ATP, and a binary complex with ATP in the presence of Mg(2+). In the monomeric conformation, AtRBSK is highly homologous to bacterial RBSKs, including the binding sites for a monovalent cation, ribose, and ATP. Its dimeric conformation, however, does not exhibit the noticeable ligand-induced changes that were observed in bacterial orthologs. Only in the presence of Mg(2+), ATP in the binary complex adopts a catalytically competent conformation, providing a mode of action for Mg(2+) in AtRBSK activity. The structural data combined with activity analyses of mutants allowed assignment of functional roles for the active site residues. Overall, this study provides the first structural characterization of plant RBSK, and experimentally validates a previous hypothetical model concerning the general reaction mechanism of RBSK. | |||
Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana.,Kang PA, Oh J, Lee H, Witte CP, Rhee S J Struct Biol. 2019 Feb 26. pii: S1047-8477(19)30030-9. doi:, 10.1016/j.jsb.2019.02.007. PMID:30822455<ref>PMID:30822455</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 6ils" style="background-color:#fffaf0;"></div> | ||
[[Category: Oh | |||
[[Category: | ==See Also== | ||
*[[Ribokinase|Ribokinase]] | |||
*[[Ribokinase 3D structures|Ribokinase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Arabidopsis thaliana]] | |||
[[Category: Large Structures]] | |||
[[Category: Kang P]] | |||
[[Category: Oh J]] | |||
[[Category: Rhee S]] | |||
Latest revision as of 12:45, 22 November 2023
Structure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATPStructure of Arabidopsis thaliana Ribokinase complexed with Ribose and ATP
Structural highlights
FunctionRBSK_ARATH Catalyzes the phosphorylation of ribose at O-5 in a reaction requiring ATP and magnesium. The resulting D-ribose-5-phosphate can then be used either for sythesis of nucleotides, histidine, and tryptophan, or as a component of the pentose phosphate pathway (By similarity) (PubMed:27601466). Can also use xylose and fructose as carbohydrate substrates with a low efficiency (PubMed:27601466). Can use GTP, and, to a lower extent, CTP and UTP as alternative phosphoryl donors (PubMed:27601466).[HAMAP-Rule:MF_03215][1] Publication Abstract from PubMedNitrogen remobilization is a key issue in plants. Recent studies in Arabidopsis thaliana have revealed that nucleoside catabolism supplies xanthine, a nitrogen-rich compound, to the purine ring catabolic pathway, which liberates ammonia from xanthine for reassimilation into amino acids. Similarly, pyrimidine nuclosides are degraded and the pyrimidine bases are fully catabolized. During nucleoside hydrolysis, ribose is released, and ATP-dependent ribokinase (RBSK) phosphorylates ribose to ribose-5'-phosphate to allow its entry into central metabolism recycling the sugar carbons from nucleosides. In this study, we report the crystal structure of RBSK from Arapidopsis thaliana (AtRBSK) in three different ligation states: an unliganded state, a ternary complex with ribose and ATP, and a binary complex with ATP in the presence of Mg(2+). In the monomeric conformation, AtRBSK is highly homologous to bacterial RBSKs, including the binding sites for a monovalent cation, ribose, and ATP. Its dimeric conformation, however, does not exhibit the noticeable ligand-induced changes that were observed in bacterial orthologs. Only in the presence of Mg(2+), ATP in the binary complex adopts a catalytically competent conformation, providing a mode of action for Mg(2+) in AtRBSK activity. The structural data combined with activity analyses of mutants allowed assignment of functional roles for the active site residues. Overall, this study provides the first structural characterization of plant RBSK, and experimentally validates a previous hypothetical model concerning the general reaction mechanism of RBSK. Crystal structure and mutational analyses of ribokinase from Arabidopsis thaliana.,Kang PA, Oh J, Lee H, Witte CP, Rhee S J Struct Biol. 2019 Feb 26. pii: S1047-8477(19)30030-9. doi:, 10.1016/j.jsb.2019.02.007. PMID:30822455[2] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences
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