ArticleThe Journal of biological chemistry2012
Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1.
Article in The Journal of biological chemistry, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 26 citations in OpenAlex.
- A pentose bisphosphate pathway of nucleotide degradation in Promethearchaeum syntrophicum.Science China. Life sciences · 2026Article
- Surviving and Adapting to Stress: Translational Control and the Integrated Stress Response.Antioxidants & redox signaling · 2023Review
- Sugar phosphate activation of the stress sensor eIF2B.Nature communications · 2021Article
- Structural preferences of cysteine sulfinic acid: The sulfinate engages in multiple local interactions with the peptide backbone.Free radical biology & medicine · 2020Article
- An overview of 25 years of research on Thermococcus kodakarensis, a genetically versatile model organism for archaeal research.Folia microbiologica · 2020Review
- The Prodigal Compound: Return of Ribosyl 1,5-Bisphosphate as an Important Player in Metabolism.Microbiology and molecular biology reviews : MMBR · 2019Review
- Role of Structural Features in Oligomerization, Active-Site Integrity and Ligand Binding of Ribose-1,5-Bisphosphate Isomerase.Computational and structural biotechnology journal · 2019Article
- A presumed homologue of the regulatory subunits of eIF2B functions as ribose-1,5-bisphosphate isomerase in Pyrococcus horikoshii OT3.Scientific reports · 2018Article
- Novel mechanisms of eIF2B action and regulation by eIF2α phosphorylation.Nucleic acids research · 2017Article
- Article
- Architecture of the eIF2B regulatory subcomplex and its implications for the regulation of guanine nucleotide exchange on eIF2.Nucleic acids research · 2015Article
- A pentose bisphosphate pathway for nucleoside degradation in Archaea.Nature chemical biology · 2015Article
- Insights into the architecture of the eIF2Bα/β/δ regulatory subcomplex.Biochemistry · 2014Article
- Carbohydrate metabolism in Archaea: current insights into unusual enzymes and pathways and their regulation.Microbiology and molecular biology reviews : MMBR · 2014Review
- An uncharacterized member of the ribokinase family in Thermococcus kodakarensis exhibits myo-inositol kinase activity.The Journal of biological chemistry · 2013Article
- Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway.Journal of bacteriology · 2012Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Ribose-1,5-bisphosphate isomerase (R15Pi) is a novel enzyme recently identified as a member of an AMP metabolic pathway in archaea. The enzyme converts d-ribose 1,5-bisphosphate into ribulose 1,5-bisphosphate, providing the substrate for archaeal ribulose-1,5-bisphosphate carboxylase/oxygenases. We here report the crystal structures of R15Pi from Thermococcus kodakarensis KOD1 (Tk-R15Pi) with and without its substrate or product. Tk-R15Pi is a hexameric enzyme formed by the trimerization of dimer units. Biochemical analyses show that Tk-R15Pi only accepts the α-anomer of d-ribose 1,5-bisphosphate and that Cys(133) and Asp(202) residues are essential for ribulose 1,5-bisphosphate production. Comparison of the determined structures reveals that the unliganded and product-binding structures are in an open form, whereas the substrate-binding structure adopts a closed form, indicating domain movement upon substrate binding. The conformational change to the closed form optimizes active site configuration and also isolates the active site from the solvent, which may allow deprotonation of Cys(133) and protonation of Asp(202) to occur. The structural features of the substrate-binding form and biochemical evidence lead us to propose that the isomerase reaction proceeds via a cis-phosphoenolate intermediate.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.