6d13 | pdb_00006d13

Crystal structure of E.coli RppH-DapF complex

spinqualitylabelsall models 6d13, resolution 3.06Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 6d13 is a 2 chain structure with sequence from Eco45. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CL, IOD Gene: dapF, ECS88_4235 (ECO45), rppH, nudH, ECS88_3125 (ECO45) Activity: Diaminopimelate epimerase, with EC number 5.1.1.7 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function [DAPF_ECO45] Catalyzes the stereoinversion of LL-2,6-diaminoheptanedioate (L,L-DAP) to meso-diaminoheptanedioate (meso-DAP), a precursor of L-lysine and an essential component of the bacterial peptidoglycan. [RPPH_ECO45] Accelerates the degradation of transcripts by removing pyrophosphate from the 5'-end of triphosphorylated RNA, leading to a more labile monophosphorylated state that can stimulate subsequent ribonuclease cleavage. Publication Abstract from PubMed Vitally important for controlling gene expression in eukaryotes and prokaryotes, the deprotection of mRNA 5' termini is governed by enzymes whose activity is modulated by interactions with ancillary factors. In Escherichia coli, 5'-end-dependent mRNA degradation begins with the generation of monophosphorylated 5' termini by the RNA pyrophosphohydrolase RppH, which can be stimulated by DapF, a diaminopimelate epimerase involved in amino acid and cell wall biosynthesis. We have determined crystal structures of RppH-DapF complexes and measured rates of RNA deprotection. These studies show that DapF potentiates RppH activity in two ways, depending on the nature of the substrate. Its stimulatory effect on the reactivity of diphosphorylated RNAs, the predominant natural substrates of RppH, requires a substrate long enough to reach DapF in the complex, while the enhanced reactivity of triphosphorylated RNAs appears to involve DapF-induced changes in RppH itself and likewise increases with substrate length. This study provides a basis for understanding the intricate relationship between cellular metabolism and mRNA decay and reveals striking parallels with the stimulation of decapping activity in eukaryotes. Structural and kinetic insights into stimulation of RppH-dependent RNA degradation by the metabolic enzyme DapF.,Gao A, Vasilyev N, Luciano DJ, Levenson-Palmer R, Richards J, Marsiglia WM, Traaseth NJ, Belasco JG, Serganov A Nucleic Acids Res. 2018 May 4. pii: 4992646. doi: 10.1093/nar/gky327. PMID:29733359 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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