PDBsum entry: 1dy5

Hydrolase

PDB id: 1dy5

Contents

Protein chains

124 a.a. *

Ligands

SO4 ×3

ACT ×4

IPA ×8

Waters ×381

* Residue conservation analysis

PDB id:

1dy5

Name:

Hydrolase

Title:

Deamidated derivative of bovine pancreatic ribonuclease

Structure:

Ribonuclease a. Chain: a, b. Mutation: yes. Other_details: asn 67 replaced by a beta-aspartyl residue

Source:

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

Resolution:

0.87Å R-factor: 0.101 R-free: 0.119

Authors:

L.Esposito,L.Vitagliano,F.Sica,A.Zagari,L.Mazzarella

Key ref:

L.Esposito et al. (2000). The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis. J Mol Biol, 297, 713-732. PubMed id: 10731423 DOI: 10.1006/jmbi.2000.3597

Date:

27-Jan-00 Release date: 28-Mar-00

Protein chains

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic

Seq: 150 a.a.

Struc: 124 a.a.*

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

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: 10.1006/jmbi.2000.3597

J Mol Biol 297:713-732 (2000)

PubMed id: 10731423

The ultrahigh resolution crystal structure of ribonuclease A containing an isoaspartyl residue: hydration and sterochemical analysis.

L.Esposito, L.Vitagliano, F.Sica, G.Sorrentino, A.Zagari, L.Mazzarella.

ABSTRACT

Crystals of the deamidated form of bovine pancreatic ribonuclease which contains an isoaspartyl residue in position 67 diffract to 0. 87 A at 100 K. We have refined the crystallographic model using anisotropic displacement parameters for all atoms to a conventional crystallographic residual R=0.101 for all observed reflections in the resolution range 61.0-0.87 A. The ratio observations/parameters is 7.2 for the final model. This structure represents one of the highest resolution protein structures to date and interestingly, it is the only example containing more than one molecule in the asymmetric unit with a resolution better than 1.0 A. The non-crystallographic symmetry has been used as a validation check of the geometrical parameters and it has allowed an estimate for an upper limit of errors associated with this high resolution model. In the present structure it was possible to obtain a more accurate picture of the active site whose electron density was not clearly interpretable in the previous 1.9 A resolution structure. In particular, the P1 site is alternatively occupied either by a sulphate anion or by a water molecule network. Most of hydrogen atoms were visible in the electron density maps, including those involved in C(alpha)-H(alpha).O interactions. Analysis of protein-solvent interactions has revealed the occurrence of an extensive cluster of water molecules, predominantly arranged in pentagonal fused rings and surrounding hydrophobic moiety of side-chains. Finally, in spite of the limited sample of residues, we have detected a clear dependence of backbone N-C(alpha)-C angle on residue conformation. This correlation can be fruitfully used as a valuable tool in protein structure validation.

Selected figure(s)

Figure 1.
Figure 1. Electron density for hydrogen atoms. (a) F[o] -F[c] map (magenta) around His12 calculated before the inclusion of hydrogen atoms in the refinement and contoured at a level of 1.7s. The difference map is superimposed to the 3F[o] -2F[c] map contoured at a level of 3.7s (cyan). (b) F[o] -F[c] map (at 3sigma level) showing H atoms involved in CA--H...O contacts in beta-sheet regions. The map has been calculated from the final model omitting all the hydrogen atoms.

Figure 4.
Figure 4. Isoaspartyl residue environment. (a) Carboxyl-carboxylate interaction between Glu A86 and isoAsp B67. Electron density map with coefficients (3F[o] -2F[c]) is contoured at 2.4sigma. (b) Highly defined electron density map in the region of the Cys A65-Cys A72 loop (contour level 2.8sigma).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 297, 713-732) copyright 2000.

Figures were selected by the author.