PDBsum entry: 1aqp

Hydrolase (phosphoric diester)

PDB id: 1aqp

Contents

Protein chain

124 a.a. *

Metals

_CU ×2

Waters ×249

* Residue conservation analysis

PDB id:

1aqp

Name:

Hydrolase (phosphoric diester)

Title:

Ribonuclease a copper complex

Structure:

Ribonuclease a. Chain: a. Synonym: rnase a. Other_details: copper complex

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas

Biol. unit:

Dimer (from PQS)

Resolution:

2.00Å R-factor: 0.200

Authors:

N.Ramasubbu

Key ref:

R.Balakrishnan et al. (1997). Crystal structures of the copper and nickel complexes of RNase A: metal-induced interprotein interactions and identification of a novel copper binding motif. Proc Natl Acad Sci U S A, 94, 9620-9625. PubMed id: 9275172 DOI: 10.1073/pnas.94.18.9620

Date:

31-Jul-97 Release date: 27-May-98

Protein chain

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic

Seq: 150 a.a.

Struc: 124 a.a.

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 (6 terms)

DOI no: 10.1073/pnas.94.18.9620

Proc Natl Acad Sci U S A 94:9620-9625 (1997)

PubMed id: 9275172

Crystal structures of the copper and nickel complexes of RNase A: metal-induced interprotein interactions and identification of a novel copper binding motif.

R.Balakrishnan, N.Ramasubbu, K.I.Varughese, R.Parthasarathy.

ABSTRACT

We report the crystal structures of the copper and nickel complexes of RNase A. The overall topology of these two complexes is similar to that of other RNase A structures. However, there are significant differences in the mode of binding of copper and nickel. There are two copper ions per molecule of the protein, but there is only one nickel ion per molecule of the protein. Significant changes occur in the interprotein interactions as a result of differences in the coordinating groups at the common binding site around His-105. Consequently, the copper- and nickel-ion-bound dimers of RNase A act as nucleation sites for generating different crystal lattices for the two complexes. A second copper ion is present at an active site residue His-119 for which all the ligands are from one molecule of the protein. At this second site, His-119 adopts an inactive conformation (B) induced by the copper. We have identified a novel copper binding motif involving the alpha-amino group and the N-terminal residues.

Selected figure(s)

Figure 1.
Fig. 1. Stereo view of the coordination spheres at the metal binding sites in the complexes. (A) Copper at the His-105 site. (B) Nickel at the His-105 site. (C) Copper at the His-119 site.

Figure 4.
Fig. 4. Superposition of the atoms N1 and the copper metal ions in the copper binding motif involving the -amino terminus and ligands from the first two residues in Gly-Gly-Gly (broken line), thioredoxin (light line), and RNase-Cu structures (thick line).

Figures were selected by an automated process.