1b2m
From Proteopedia
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THREE-DIMENSIONAL STRUCTURE OF RIBONULCEASE T1 COMPLEXED WITH AN ISOSTERIC PHOSPHONATE ANALOGUE OF GPU: ALTERNATE SUBSTRATE BINDING MODES AND CATALYSIS.
Overview
The X-ray crystal structure of a complex between ribonuclease T1 and, guanylyl(3'-6')-6'-deoxyhomouridine (GpcU) has been determined at 2. 0 A, resolution. This ligand is an isosteric analogue of the minimal RNA, substrate, guanylyl(3'-5')uridine (GpU), where a methylene is substituted, for the uridine 5'-oxygen atom. Two protein molecules are part of the, asymmetric unit and both have a GpcU bound at the active site in the same, manner. The protein-protein interface reveals an extended aromatic stack, involving both guanines and three enzyme phenolic groups. A third GpcU has, its guanine moiety stacked on His92 at the active site on enzyme molecule, A and interacts with GpcU on molecule B in a neighboring unit via hydrogen, bonding between uridine ribose 2'- and 3'-OH groups. None of the uridine, moieties of the three GpcU molecules in the asymmetric unit interacts, directly with the protein. GpcU-active-site interactions involve extensive, hydrogen bonding of the guanine moiety at the primary recognition site and, of the guanosine 2'-hydroxyl group with His40 and Glu58. On the other, hand, the phosphonate group is weakly bound only by a single hydrogen bond, with Tyr38, unlike ligand phosphate groups of other substrate analogues, and 3'-GMP, which hydrogen-bonded with three additional active-site, residues. Hydrogen bonding of the guanylyl 2'-OH group and the phosphonate, moiety is essentially the same as that recently observed for a novel, structure of a RNase T1-3'-GMP complex obtained immediately after in situ, hydrolysis of exo-(Sp)-guanosine 2',3'-cyclophosphorothioate [Zegers et, al. (1998) Nature Struct. Biol. 5, 280-283]. It is likely that GpcU at the, active site represents a nonproductive binding mode for GpU [Steyaert, J., and Engleborghs (1995) Eur. J. Biochem. 233, 140-144]. The results suggest, that the active site of ribonuclease T1 is adapted for optimal tight, binding of both the guanylyl 2'-OH and phosphate groups (of GpU) only in, the transition state for catalytic transesterification, which is, stabilized by adjacent binding of the leaving nucleoside (U) group.
About this Structure
1B2M is a Single protein structure of sequence from Aspergillus oryzae. Active as Ribonuclease T(1), with EC number 3.1.27.3 Full crystallographic information is available from OCA.
Reference
Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis., Arni RK, Watanabe L, Ward RJ, Kreitman RJ, Kumar K, Walz FG Jr, Biochemistry. 1999 Feb 23;38(8):2452-61. PMID:10029539
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