PDBsum entry 5rnt

Hydrolase(endoribonuclease)

PDB id: 5rnt

Contents

Protein chain

104 a.a. *

Ligands

PGP

Waters ×83

* Residue conservation analysis

PDB id:

5rnt

Name:

Hydrolase(endoribonuclease)

Title:

X-ray analysis of cubic crystals of the complex formed between ribonuclease t1 and guanosine-3',5'-bisphosphate

Structure:

Ribonuclease t1. Chain: a. Engineered: yes

Source:

Aspergillus oryzae. Organism_taxid: 5062

Resolution:

3.20Å R-factor: 0.166

Authors:

W.Saenger,U.Heinemann,A.Lenz

Key ref:

A.Lenz et al. (1991). X-ray analysis of cubic crystals of the complex formed between ribonuclease T1 and guanosine-3',5'-bisphosphate. Acta Crystallogr B, 47, 521-527. PubMed id: 1930833

Date:

28-Mar-91 Release date: 15-Jan-93

Protein chain

P00651  (RNT1_ASPOR) -  Guanyl-specific ribonuclease T1 from Aspergillus oryzae (strain ATCC 42149 / RIB 40)

Seq: 130 a.a.

Struc: 104 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.6.1.24 - ribonuclease T1.
• Reaction: [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]

Acta Crystallogr B 47:521-527 (1991)

PubMed id: 1930833

X-ray analysis of cubic crystals of the complex formed between ribonuclease T1 and guanosine-3',5'-bisphosphate.

A.Lenz, U.Heinemann, M.Maslowska, W.Saenger.

ABSTRACT

The complex formed between ribonuclease T1 (RNase T1) and guanosine-3',5'-bisphosphate (3',5'-pGp) crystallizes in the cubic space group I23 with alpha = 86.47 (4) A. X-ray data were collected on a four-circle diffractometer to 3.2 A resolution and the structure was determined by molecular-replacement methods [ULTIMA; Rabinovich & Shakked (1984). Acta Cryst. A40, 195-200] based on the RNase T1 coordinates taken from the complex with guanosine-2'-phosphate. Refinement converged at 16.6% for 1540 data with Fo greater than 1 sigma (Fo) with acceptable stereochemistry. The RNase T1 conformation is comparable to that in other complexes which crystallize preferentially in space group P2(1)2(1)2(1) except for side chains that interact intermolecularly. The guanine of 3',5'-pGp is bound to the recognition site in the same way as in other guanine-containing complexes except for its interaction with Glu46. The side-chain carboxylate of this amino acid does not form hydrogen bonds to N1H and N2H of guanine but is rotated so as to permit insertion of two water molecules which replace its acceptor functions. In contrast to other guanosine derivatives which are bound to RNase T1 in the syn form, 3',5'-pGp is anti. This conformation positions the two phosphate groups 'outside' the protein, with hydrogen-bonding contacts only to water molecules; the active site is filled by water. The RNase T1-3',5'-pGp complex probably has biological significance as it may represent the enzyme-product complex before dissociation.