PDBsum entry 1kf8

Hydrolase

PDB id: 1kf8

Contents

Protein chain

124 a.a. *

Waters ×235

* Residue conservation analysis

PDB id:

1kf8

Name:

Hydrolase

Title:

Atomic resolution structure of rnase a at ph 8.8

Structure:

Pancreatic ribonuclease. Chain: a. Synonym: rnase a. Ec: 3.1.27.5

Source:

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

Resolution:

1.15Å R-factor: 0.106

Authors:

R.Berisio,F.Sica,V.S.Lamzin,K.S.Wilson,A.Zagari,L.Mazzarella

Key ref:

R.Berisio et al. (2002). Atomic resolution structures of ribonuclease A at six pH values. Acta Crystallogr D Biol Crystallogr, 58, 441-450. PubMed id: 11856829 DOI: 10.1107/S0907444901021758

Date:

19-Nov-01 Release date: 19-Dec-01

Protein chain

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic from Bos taurus

Seq: 150 a.a.

Struc: 124 a.a.

Enzyme reactions

• Enzyme class: E.C.4.6.1.18 - pancreatic ribonuclease.
• Reaction:
  1. an [RNA] containing cytidine + H2O = an [RNA]-3'-cytidine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]
  2. an [RNA] containing uridine + H2O = an [RNA]-3'-uridine-3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA]

DOI no: 10.1107/S0907444901021758

Acta Crystallogr D Biol Crystallogr 58:441-450 (2002)

PubMed id: 11856829

Atomic resolution structures of ribonuclease A at six pH values.

R.Berisio, F.Sica, V.S.Lamzin, K.S.Wilson, A.Zagari, L.Mazzarella.

ABSTRACT

The diffraction pattern of protein crystals extending to atomic resolution guarantees a very accurate picture of the molecular structure and enables the study of subtle phenomena related to protein functionality. Six structures of bovine pancreatic ribonuclease at the pH* values 5.2, 5.9, 6.3, 7.1, 8.0 and 8.8 and at resolution limits in the range 1.05-1.15A have been refined. An overall description of the six structures and several aspects, mainly regarding pH-triggered conformational changes, are described here. Since subtle variations were expected, a thorough validation assessment of the six refined models was first carried out. Some stereochemical parameters, such as the N[bond]C(alpha)[bond]C angle and the pyramidalization at the carbonyl C atoms, indicate that the standard target values and their weights typically used in refinement may need revision. A detailed comparison of the six structures has provided experimental evidence on the role of Lys41 in catalysis. Furthermore, insights are given into the structural effects related to the pH-dependent binding of a sulfate anion, which mimics the phosphate group of RNA, in the active site. Finally, the results support a number of thermodynamic and kinetic experimental data concerning the role of the disulfide bridge between Cys65 and Cys72 in the folding of RNase A.

Selected figure(s)

Figure 3.
Figure 3 Conformational changes of the catalytic Gln11 and Lys41. (a) Superposition of the two structures at pH* 5.2 (dark grey) and 8.0 (light grey); only the most populated conformers are shown for clarity. (b) Electron-density maps (3F[o] - 2F[c]) contoured at 1.7 for the structures at pH* 5.2 and (c) at pH* 8.8. The figures were generated using the program BOBSCRIPT (Esnouf, 1999[Esnouf, R. M. (1999). Acta Cryst. D55, 938-940.]).

Figure 6.
Figure 6 Electron-density map (3F[o] - 2F[c]), contoured at 2.7 , showing the double conformation of the disulfide bridge [65-72].

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2002, 58, 441-450) copyright 2002.

Figures were selected by an automated process.