Modomics - A Database of RNA Modifications

ID Card:

Full name: NADPH-dependent 7-cyano-7-deazaguanine reductase
Synonym: ykvM, BSU13750
GI: 81555909
COG: COG0780
UniProt: O31678
Structures: | 4F8B | 4FGC | 5UDG |
Enzyme type: oxidoreductase
Position of modification - modification: t:34 - Q

PDB Structures:


Structure Description:


Abstract of the PDB Structure's related Publication:

The enzyme QueF catalyzes the reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ(0)) to 7-aminomethyl-7-deazaguanine (preQ(1)), the only nitrile reduction reaction known in biology. We describe here two crystal structures of Bacillus subtilis QueF, one of the wild-type enzyme in complex with the substrate preQ(0), trapped as a covalent thioimide, a putative intermediate in the reaction, and the second of the C55A mutant in complex with the substrate preQ(0) bound noncovalently. The QueF enzyme forms an asymmetric tunnel-fold homodecamer of two head-to-head facing pentameric subunits, harboring 10 active sites at the intersubunit interfaces. In both structures, a preQ(0) molecule is bound at eight sites, and in the wild-type enzyme, it forms a thioimide covalent linkage to the catalytic residue Cys-55. Both structural and transient kinetic data show that preQ(0) binding, not thioimide formation, induces a large conformational change in and closure of the active site. Based on these data, we propose a mechanism for the activation of the Cys-55 nucleophile and subsequent hydride transfer.

Download RCSB-PDB Structures:

Pdb Files   4F8B.pdb   4FGC.pdb   5UDG.pdb  
Pdbx/mmCIF Files   4F8B.cif   4FGC.cif   5UDG.cif  

Protein sequence:



Reaction Substrate SubstrateType Position (Anti)Codon Modified (Anti)Codon Amino Acid Change Transcript Name Transcript Region Cellular Localization References
preQ0base:preQ1base     17929836   


Title Authors Journal Details PubMed Id DOI
Crystallization and preliminary X-ray characterization of the nitrile reductase QueF: a queuosine-biosynthesis enzyme. Swairjo MA, Reddy RR, Lee B, Van Lanen SG, Brown S, de Crecy-Lagard V, Iwata-Reuyl D, Schimmel P Acta Crystallogr Sect F Struct Biol Cryst Commun [details] 16511203 -
From cyclohydrolase to oxidoreductase: discovery of nitrile reductase activity in a common fold. Van Lanen SG, Reader JS, Swairjo MA, de Crecy-Lagard V, Lee B, Iwata-Reuyl D Proc Natl Acad Sci U S A [details] 15767583 -
Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. Reader JS, Metzgar D, Schimmel P, de Crecy-Lagard V J Biol Chem [details] 14660578 -
Mechanistic studies of Bacillus subtilis QueF, the nitrile oxidoreductase involved in queuosine biosynthesis. Lee BW, Van Lanen SG, Iwata-Reuyl D Biochemistry [details] 17929836 -
Structural Basis of Biological Nitrile Reduction. Chikwana VM, Stec B, Lee BW, de Crecy-Lagard V, Iwata-Reuyl D, Swairjo MA J Biol Chem [details] 22787148 -