PDBsum entry: 1dza

Hydrolase

PDB id: 1dza

Contents

Protein chains

121 a.a. *

Waters ×273

* Residue conservation analysis

PDB id:

1dza

Name:

Hydrolase

Title:

3-d structure of a hp-rnase

Structure:

Ribonuclease 1. Chain: a, b. Synonym: rnase 1, hp-rnase. Engineered: yes. Mutation: yes. Other_details: 100a formilmethionine (fme)

Source:

Homo sapiens. Human. Organism_taxid: 9606. Organ: pancreas. Plasmid: pm7. Gene: pm7. Expressed in: escherichia coli. Expression_system_taxid: 469008. Other_details: synthetic gene

Resolution:

1.65Å R-factor: 0.177 R-free: 0.236

Authors:

J.Pous,A.Canals,S.S.Terzyan,A.Guasch,A.Benito,M.Ribo, M.Vilanova,M.Coll

Key ref:

J.Pous et al. (2000). Three-dimensional structure of a human pancreatic ribonuclease variant, a step forward in the design of cytotoxic ribonucleases. J Mol Biol, 303, 49-60. PubMed id: 11021969 DOI: 10.1006/jmbi.2000.4506

Date:

21-Feb-00 Release date: 16-Feb-01

Protein chains

P07998  (RNAS1_HUMAN) -  Ribonuclease pancreatic

Seq: 156 a.a.

Struc: 121 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.27.5 - Pancreatic ribonuclease.
• Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides ending in C-P or U-P with 2',3'-cyclic phosphate intermediates.

 Gene Ontology (GO) functional annotation 

• Cellular component: extracellular region (1 term)
• Biochemical function: nucleic acid binding (5 terms)

DOI no: 10.1006/jmbi.2000.4506

J Mol Biol 303:49-60 (2000)

PubMed id: 11021969

Three-dimensional structure of a human pancreatic ribonuclease variant, a step forward in the design of cytotoxic ribonucleases.

J.Pous, A.Canals, S.S.Terzyan, A.Guasch, A.Benito, M.Ribó, M.Vilanova, M.Coll.

ABSTRACT

We have determined the crystal structure of a human pancreatic ribonuclease or RNase 1 variant at 1.65 A resolution. Five residues in the N-terminal region were substituted by the corresponding amino acids of the bovine seminal RNase. In addition, a Pro to Ser mutation was present at position 50. The substitution of part of the N terminus has been critical both in improving the expression of this enzyme as a recombinant protein and in achieving its crystallisation. The determination of the crystal structure revealed the characteristic RNase fold including a V-shaped beta-sheet and three alpha-helices. It differs from its bovine RNase orthologue mainly in the loop regions. The active-site cleft shows a similar architecture to that of its bovine counterpart, with the essential residues occupying equivalent positions. In the present structure, however, His119 is displaced as it is in the structure of RNase A at high pH. An interaction model of human ribonuclease with the ribonuclease inhibitor, together with inhibition assays, indicate that, in contrast to RNase A, the modification of the loop beta4beta5 is not enough to avoid inhibition. This study represents the first crystallographic approach to the human enzyme, and should constitute an invaluable tool for the design of ribonuclease variants with acquired cytotoxic properties.

Selected figure(s)

Figure 4.
Figure 4. Protein-protein interactions. (a) and (b) Electrostatic surface of PM7 showing the acidic patch (a) that interacts with the basic active-site cleft (b) of molecules A and B in the asymmetric unit. (c) Molecules A and B as they pack in the crystal, with one molecule occupying the active site cleft of the other. (d) Electrostatic surface show- ing interaction between neighbouring molecules A and B from different asymmetric units which closely resembles the swapped dimer of RNase A. The Figures were generated with GRASP (Nicholls et al., 1991).

Figure 5.
Figure 5. Superimposed structures of molecules A (blue) and B (yellow) of PM7, and RNase A (red; PDB code 7RSA) at the loop b4-b5. Common residues are labelled in black, whereas differences in the primary structure are highlighted by the use of labels coloured according to the molecule.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 303, 49-60) copyright 2000.

Figures were selected by the author.