Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.
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 preQ0forms 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 preQ0binding 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. © 2016 Wiley Periodicals, Inc.
Department of Chemistry and Biochemistry, San Diego State University- 5500 Campanile Drive, San Diego, California, 92182.
Xianghan
X
Mei
Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California, 91766-1854.
Jonathan
J
Alvarez
Department of Chemistry, Portland State University, Portland, Oregon, 97207.
Adriana
A
Bon Ramos
Graduate College of Biomedical Sciences, Western University of Health Sciences, Pomona, California, 91766-1854.
Uttamkumar
U
Samanta
Department of Chemistry, Portland State University, Portland, Oregon, 97207.
Dirk
D
Iwata-Reuyl
Department of Chemistry and Biochemistry, San Diego State University- 5500 Campanile Drive, San Diego, California, 92182.
Manal A
MA
Swairjo
D000579:Amidinotransferases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D020134:Catalytic Domain; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D006151:Guanosine / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D062105:Molecular Docking Simulation; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D000072757:Protein Conformation, beta-Strand; D054730:Protein Interaction Domains and Motifs; D055503:Protein Multimerization; D021122:Protein Subunits / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011744:Pyrimidinones / Q000737:chemistry* / Q000378:metabolism; D041543:Pyrobaculum / Q000201:enzymology* / Q000235:genetics; D011758:Pyrroles / Q000737:chemistry* / Q000378:metabolism; D012323:RNA Processing, Post-Transcriptional; D019642:RNA, Archaeal / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D013379:Substrate Specificity
C586109:2-amino-5-cyanopyrrolo(2,3-d)pyrimidin-4-one; D019843:Archaeal Proteins; D021122:Protein Subunits; D011744:Pyrimidinones; D011758:Pyrroles; D019642:RNA, Archaeal; D011994:Recombinant Proteins; D006151:Guanosine; C081066:archaeosine; D012343:RNA, Transfer; D000579:Amidinotransferases
7-cyano-7-deazaguanine; 7-deazaguanosine; QueF-L; T-fold; amidinotransferase; modified nucleoside; preQ0; thioimide; transfer-RNA; tunneling-fold enzyme