5JYX

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

Summary for 5JYX

• Entry DOI: 10.2210/pdb5jyx/pdb
• Related: 5K0P
• Descriptor: Archeaosine synthase QueF-Like, 2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one, SODIUM ION, ... (4 entities in total)
• Functional Keywords: thioimide, amidinotransferase, c2 space group, hydrolase, transferase
• Biological source: Pyrobaculum calidifontis
• Total number of polymer chains: 15
• Total formula weight: 185199.54

Authors

Mei, X.,Swairjo, M.A. (deposition date: 2016-05-15, release date: 2016-11-09, Last modification date: 2024-11-06)

Primary citation

Mei, X.,Alvarez, J.,Bon Ramos, A.,Samanta, U.,Iwata-Reuyl, D.,Swairjo, M.A.
Crystal structure of the archaeosine synthase QueF-like-Insights into amidino transfer and tRNA recognition by the tunnel fold.
Proteins, 85:103-116, 2017

PubMed Abstract: 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 (preQ ) base of preQ -modified tRNA to a formamidino group. The structure, determined in the presence of preQ , reveals a symmetric T-fold homodecamer of two head-to-head facing pentameric subunits, with 10 active sites at the inter-monomer interfaces. Bound preQ 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 preQ 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. © 2016 Wiley Periodicals, Inc.

PubMed: 27802572
DOI: 10.1002/prot.25202

Experimental method

X-RAY DIFFRACTION (2.74 Å)