The complex between ribonuclease T1 and 3′GMP suggests geometry of enzymic reaction path

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Abstract
The crystal structure of the complex between ribonuclease T1 and 3′GMP suggests that (a) a substrate GpN is bound to the active site of ribonuclease T1 in a conformation that actively supports the catalytic process, (b) the reaction occurs in an in‐line process, (c) His40 NɛH+ activates O2′‐H, (d) Glu58 carboxylate acts as base and His92 NɛH+ as acid in a general acid‐base catalysis. The crystals have the monoclinic space group P21, a= 4.968 nm, b= 4.833 nm, c= 4.048 nm, β= 90.62° with two molecules in the asymmetric unit. The structure was determined by molecular replacement and refined to R= 15.3% with 11338 data ≥1σ(F°) in the resolution range 1.0–0.2 nm; this includes 180 water molecules and two Ca2+. The structure of ribonuclease T1 is as previously observed. 3′GMP is bound in syn conformation; guanine is located in the specific recognition site, the ribose adopts C4′‐exo puckering, the ribose phosphate is extended with torsion angle ɛ in trans. The O2′‐H group is activated by accepting and donating hydrogen bonds from His40 NɛH+ and to Glu58 Oɛ1; the phosphate is hydrogen bonded to Glu58 Oɛ2H, Arg77 NɛH+ and Nη2H+, Tyr38 OηH, His92 NɛH+. The conformation of ribose phosphate is such that O2′ is at a distance of 0.31 nm from phosphorus, and opposite the P‐OP3 bond which accepts a hydrogen bond from His92 NɛH+; we infer from a model building study that this bond is equivalent to the scissile P‐O5′ in a substrate GpN.