Three-dimensional structure of ribonuclease T1 complexed with an isosteric phosphonate substrate analogue of GpU: alternate substrate binding modes and catalysis.Arni, R.K., Watanabe, L., Ward, R.J., Kreitman, R.J., Kumar, K., Walz Jr., F.G.
(1999) Biochemistry 38: 2452-2461
- PubMed: 10029539
- DOI: 10.1021/bi982612q
- Primary Citation of Related Structures:
- PubMed Abstract:
- Three-Dimensional Structure of Gln 25-Ribonuclease T1 at 1.84 Angstroms Resolution: Structural Variations at the Base Recognition and Catalytic Sites
Arni, R.K., Pal, G.P., Ravichandran, K.G., Tulinsky, A., Metcalf Jr., P.F.G.W.
(1992) Biochemistry 31: 3126
- Crystal Structure of Guanosine-Free Ribonuclease T1, Complexed with Vanadate(V), Suggests Conformational Change Upon Substrate Binding
Kostrewa, D., Choe, H.-W., Heinemann, U., Saenger, W.
(1989) Biochemistry 28: 7592
- Three Dimensional Structures of the Ribonuclease T1 2'-Gmp Complex at 1.9 Angstroms Resolution
Arni, R., Heinemann, U., Tokuoka, R., Saenger, W.
(1988) J Biol Chem 263: 15358
- Restrained Least-Squares Refinement of the Crystal Structure of the Ribonuclease T1 2'-Guanylic Acid Complex at 1.9 Angstroms Resolution
Arni, R., Heinemann, V., Maslowska, M., Tokuoka, R., Saenger, W.
(1987) Acta Crystallogr B 43: 548
- Structure and Function of the Enzyme Ribonuclease T1
Arni, R., Heinemann, U., Saenger, W.
(1987) Fresenius Z für Anal Chem 327: 67
- Crystallization of Ribonuclease T1
Martin, P.O., Tulinsky, A., Walz, F.G.
(1980) J Mol Biol 136: 95
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 ...
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.
Department of Physics, UNESP/IBILCE, S. J. do Rio Preto-SP, Brazil.