PDBsum entry 1gmr

Hydrolase(guanyloribonuclease)

PDB id: 1gmr

Contents

Protein chains

96 a.a. *

Ligands

SO4

2GP ×2

Waters ×388

* Residue conservation analysis

PDB id:

1gmr

Name:

Hydrolase(guanyloribonuclease)

Title:

Complex of ribonuclease from streptomyces aureofaciens with 2'-gmp at 1.7 angstroms resolution

Structure:

Ribonuclease sa. Chain: a, b. Engineered: yes

Source:

Streptomyces aureofaciens. Organism_taxid: 1894

Resolution:

1.77Å R-factor: 0.146

Authors:

J.Sevcik,C.Hill,Z.Dauter,K.Wilson

Key ref:

J.Sevcik et al. (1993). Complex of ribonuclease from Streptomyces aureofaciens with 2'-GMP at 1.7 A resolution. Acta Crystallogr D Biol Crystallogr, 49, 257-271. PubMed id: 15299531 DOI: 10.1107/S0907444992007261

Date:

01-Oct-92 Release date: 31-Oct-93

Protein chains

P05798  (RNSA_KITAU) -  Guanyl-specific ribonuclease Sa from Kitasatospora aureofaciens

Seq: 96 a.a.

Struc: 96 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]

DOI no: 10.1107/S0907444992007261

Acta Crystallogr D Biol Crystallogr 49:257-271 (1993)

PubMed id: 15299531

Complex of ribonuclease from Streptomyces aureofaciens with 2'-GMP at 1.7 A resolution.

J.Sevcik, C.P.Hill, Z.Dauter, K.S.Wilson.

ABSTRACT

The crystal structure of a complex of ribonuclease from Streptomyces aureofaciens (RNase Sa) with guanosine-2'-monophosphate (2'-GMP) has been refined against synchrotron data recorded from a single crystal using radiation from beamline X31 at EMBL, Hamburg, and an imaging plate scanner. The crystals are in space group P2(1)2(1)2(1) with cell dimensions a = 64.7, b = 78.8 and c = 39.1 A. The structure has two enzyme molecules in the asymmetric unit, complexed with 2'-GMP inhibitor with occupancies of 1 and 2/3 (different to the 3'-GMP complex crystal structure where only one of the two independent RNase Sa molecules binds nucleotide), 492 associated water molecules and one sulfate ion, and was refined using all data between 10.0 and 1.7 A to a final crystallographic R factor of 13.25%. Binding of the base to the enzyme confirms the basis for the guanine specificity but the structural results still do not provide direct evidence of the identity and role of the particular residues involved in the catalytic process. New native RNase Sa data to 1.8 A were recorded to provide a reference set measured under comparable experimental conditions. The crystals are in the same space group and have the same lattice as those of the 2'-GMP complex. The native structure with 423 water molecules was refined in a similar manner to the complex to a final R factor of 13.87%. 1.77 A resolution data were independently measured on a 2'-GMP complex crystal at UCLA using an R-AXIS II image plate scanner mounted on a conventional source. The cell dimensions were essentially the same as above. 2'-GMP was bound more fully to molecule A than to molecule B of the RNase Sa. The structure was refined to an R factor of 14.64% with 388 water molecules. This work follows on from the structure determination of native RNase Sa and its complex with 3'-GMP [Sevcik, Dodson & Dodson (1991). Acta Cryst. B47, 240-253].

Selected figure(s)

Figure 11.
Fig. 11. The hydrogen-bonding network formed between the enzyme and guanine base of the EMBL 2'-GMP inhibitor in the B molecule.

Figure 13.
Fig. 13. Binding of the 2'-GMP phosphate group to molecule A. The hydrogen bonds to the hosphate oxygens are shown as thin lines.

Figure 31.
Ser 31A, Gin 32A and the side chain of Glu 54A in relation to the native enzyme. These changes are not observed n the 2'-GMP complex as the ribose ring of the inhibitor is directed towards the outside of he enzyme molecule and less structural change is neces- sary for 2'-GMP to bind t the enzyme. The largest changes caused by 2'-GMP binding are observed in the positions of residues His 85 and Tyr 86 which move towards the phosphate group in order to bind to it. These two residues are very flexible and show a degree of disorder in the native structure also. The puckers adopted by the ribose moiety in the A an B molecules in EMBL 2'-GMP and the A mol- ecule in the UCLA '-GMP are essentially identical. They are not ideal C(3')-endo conformations, ut closely similar, with the C2' atom lyng slightly above the plane of the CI', 04' and C4' atoms rather than somewhat below as in th ideal conformation (Fig. 12a). The torsion angle around the glycosyl link is in the syn conformation, in contrast to the 3'-GMP complex where a C(2')-endo pucker and the anti conformation was adopted (Fig. 12b). Indeed the riboses lie in distinctly different positions in the 2'- and 3'-GMP complexes (Fig. 10h). The pucker for the 2'-GMP in the B molecule of the UCLA model refines much closer to the ideal C(3')-endo conforma- tion (Fig. 12c). This is almost certainly a esult of the low occupacy (~) and overall higher B factor for this structure, rather than a real structral difference. The occuancy of 2'-GMP is 1 in both A molecules, and ~ m the EMBL B molecule. This again emphasizes the need of accurate high-resolution data for such detailed analyses. The binding of the phosphate group is not so specific as the binding of the base. The phosphate binding ligands are the side chains of Glu 54, Arg 65, Arg 69, His 85 and Tyr 86 (Fig. 13), which lie in a relatively flexible part of the structure equipped with a nmber of potential binding sites capable of

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (1993, 49, 257-271) copyright 1993.

Figures were selected by an automated process.