5jyx

Crystal structure of the covalent thioimide intermediate of the archaeosine synthase QueF-Like

spinqualitylabelsall models 5jyx, resolution 2.74Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5jyx is a 15 chain structure with sequence from Pyrobaculum calidifontis JCM 11548. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 2.74Å Ligands: GD1, MSE, NA Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function QUEFL_PYRCJ Is responsible for the final step in the biosynthesis of archaeosine, a modified nucleoside present in the dihydrouridine loop (D-loop) of archaeal tRNA (PubMed:22032275, PubMed:28383498). Catalyzes the conversion of 7-cyano-7-deazaguanine (preQ0)-modified tRNA to archaeosine-tRNA, transforming a nitrile group to a formamidine group. Can use neither glutamine nor asparagine as amino donor in vitro, is only able to utilize free ammonium (PubMed:28383498). However, the enzyme might function in vivo with a partner that serves to generate ammonium. Publication Abstract from PubMed The tunneling-fold (T-fold) structural superfamily has emerged as a versatile protein scaffold of diverse catalytic activities. This is especially evident in the pathways to the 7-deazaguanosine modified nucleosides of tRNA queuosine and archaeosine. Four members of the T-fold superfamily have been confirmed in these pathways and here we report the crystal structure of a fifth enzyme; the recently discovered amidinotransferase QueF-Like (QueF-L), responsible for the final step in the biosynthesis of archaeosine in the D-loop of tRNA in a subset of Crenarchaeota. QueF-L catalyzes the conversion of the nitrile group of the 7-cyano-7-deazaguanine (preQ0 ) base of preQ0 -modified tRNA to a formamidino group. The structure, determined in the presence of preQ0 , reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ0 forms a stable covalent thioimide bond with a conserved active site cysteine similar to the intermediate previously observed in the nitrile reductase QueF. Despite distinct catalytic functions, phylogenetic distributions, and only 19% sequence identity, the two enzymes share a common preQ0 binding pocket, and likely a common mechanism of thioimide formation. However, due to tight twisting of its decamer, QueF-L lacks the NADPH binding site present in QueF. A large positively charged molecular surface and a docking model suggest simultaneous binding of multiple tRNA molecules and structure-specific recognition of the D-loop by a surface groove. The structure sheds light on the mechanism of nitrile amidation, and the evolution of diverse chemistries in a common fold. Proteins 2016; 85:103-116. (c) 2016 Wiley Periodicals, Inc. Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.,Mei X, Alvarez J, Bon Ramos A, Samanta U, Iwata-Reuyl D, Swairjo MA Proteins. 2017 Jan;85(1):103-116. doi: 10.1002/prot.25202. Epub 2016 Nov 20. PMID:27802572 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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