4F8B

Crystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF

Summary for 4F8B

• Entry DOI: 10.2210/pdb4f8b/pdb
• Related: 4FGC
• Descriptor: NADPH-dependent 7-cyano-7-deazaguanine reductase, 2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: beta barrel, protein thioimide complex, pterin binding fold, tunnel fold, trna modification enzyme, 7-cyano-7-deazaguanine, nadph, oxidoreductase
• Biological source: Bacillus subtilis subsp. subtilis
• Cellular location: Cytoplasm : O31678
• Total number of polymer chains: 5
• Total formula weight: 98240.05

Authors

Stec, B.,Swairjo, M.A. (deposition date: 2012-05-17, release date: 2012-07-11, Last modification date: 2024-11-06)

Primary citation

Chikwana, V.M.,Stec, B.,Lee, B.W.,de Crecy-Lagard, V.,Iwata-Reuyl, D.,Swairjo, M.A.
Structural basis of biological nitrile reduction.
J.Biol.Chem., 287:30560-30570, 2012

PubMed Abstract: 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.

PubMed: 22787148
DOI: 10.1074/jbc.M112.388538

Experimental method

X-RAY DIFFRACTION (2.502 Å)