PDBsum entry 1bc4

Hydrolase

PDB id: 1bc4

Contents

Protein chain

111 a.a. *

* Residue conservation analysis

PDB id:

1bc4

Name:

Hydrolase

Title:

The solution structure of a cytotoxic ribonuclease from the oocytes of rana catesbeiana (bullfrog), nmr, 15 structures

Structure:

Ribonuclease. Chain: a. Synonym: rc rnase. Ec: 3.1.27.5

Source:

Rana catesbeiana. Bullfrog. Organism_taxid: 8400

NMR struc:

15 models

Authors:

C.-F.Chang,C.Chen,Y.-C.Chen,K.Hom,R.-F.Huang,T.Huang

Key ref:

C.F.Chang et al. (1998). The solution structure of a cytotoxic ribonuclease from the oocytes of Rana catesbeiana (bullfrog). J Mol Biol, 283, 231-244. PubMed id: 9761686 DOI: 10.1006/jmbi.1998.2082

Date:

05-May-98 Release date: 14-Oct-98

Protein chain

P11916  (RNASO_AQUCT) -  Oocytes ribonuclease from Aquarana catesbeiana

Seq: 133 a.a.

Struc: 111 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.3.1.27.- - ?????

DOI no: 10.1006/jmbi.1998.2082

J Mol Biol 283:231-244 (1998)

PubMed id: 9761686

The solution structure of a cytotoxic ribonuclease from the oocytes of Rana catesbeiana (bullfrog).

C.F.Chang, C.Chen, Y.C.Chen, K.Hom, R.F.Huang, T.H.Huang.

ABSTRACT

RC-RNase is a pyrimidine-guanine sequence-specific ribonuclease and a lectin possessing potent cell cytotoxicity. It was isolated from the oocytes of Rana catesbeiana (bull frog). From analysis of an extensive set of 1H homonuclear 2D NMR spectra we have completed the resonance assignments. Determination of the three-dimensional structure was carried out with the program X-PLOR using a total of 951 restraints including 814 NMR-derived distances, 61 torsion angles, and 76 hydrogen bond restraints. In the resultant family of 15 best structures, selected from a total of 150 calculated structures, the root-mean-square deviation from the average structure for the backbone heavy-atoms involved in well-defined secondary structure is 0.48 A, while that for all backbone heavy-atoms is 0.91 A. The structure of RC-RNase consists of three alpha-helices and two triple-stranded anti-parallel beta-sheets and folds in a kidney-shape, very similar to the X-ray crystal structure of a homolo gous protein, onconase isolated from Rana pipiens. We have also investigated the interaction between RC-RNase and two inhibitors, cytidylyl(2'-->5')guanosine (2',5'-CpG) and 2'-deoxycytidylyl(3'-->5')-2'-deoxyguanosine (3',5'-dCpdG). Based on the ligand-induced chemical shift changes in RC-RNase and the NOE cross-peaks between RC-RNase and the inhibitors, the key residues involved in protein-inhibitor interaction have been identified. The inhibitors were found to bind in a "retro-binding" mode, with the guanine base bonded to the B1 subsite. The His103 residue was found to occupy the B state with the imidazole ring pointing away from the active site. The structure coordinates and the NMR restraints have been deposited in the Brookhaven Protein Data Bank (1bc4 and 1bc4mr, respectively).

Selected figure(s)

Figure 7.
Figure 7. The surface structure and surface charge profile of the energy minimized, averaged structure of RC-RNase. The structure was generated with the program GRASP [Nicholls et al 1991] with partial charge taken directly from the default charge table (full.crg). Blue represents positive electrostatic potential, red represents negative electrostatic potential and white indicates charge neutral regions.

Figure 9.
Figure 9. Spatial arrangement of the residues whose proton chemical shifts change upon binding of 2',5'-CpG. These residues are labeled and are shown by van der Waals spheres.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 283, 231-244) copyright 1998.

Figures were selected by the author.