PDBsum entry: 1cjq

Hydrolase

PDB id: 1cjq

Contents

Protein chains

15 a.a.

101 a.a. *

Ligands

SO4

Waters ×7

* Residue conservation analysis

PDB id:

1cjq

Name:

Hydrolase

Title:

X-ray crystallographic studies of the denaturation of the denaturation of ribonuclease s.

Structure:

Protein (ribonuclease s). Chain: a. Fragment: s peptide. Other_details: synthetic. Protein (ribonuclease s). Chain: b. Fragment: s protein. Synonym: rnase s

Source:

Synthetic construct. Organism_taxid: 32630. Other_details: synthetic s peptide. Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.175 R-free: 0.253

Authors:

G.S.Ratnaparkhi,R.Varadarajan

Key ref:

G.S.Ratnaparkhi and R.Varadarajan (1999). X-ray crystallographic studies of the denaturation of ribonuclease S. Proteins, 36, 282-294. PubMed id: 10409822 DOI: 10.1002/(SICI)1097-0134(19990815)36:3<282::AID-PROT3>3.3.CO;2-6

Date:

19-Apr-99 Release date: 07-May-99

Protein chain

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic

Seq: 150 a.a.

Struc: 15 a.a.

Protein chain

P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic

Seq: 150 a.a.

Struc: 101 a.a.

Enzyme reactions

• Enzyme class: Chains A, B: 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 

• Biochemical function: nucleic acid binding (2 terms)

DOI no: 10.1002/(SICI)1097-0134(19990815)36:3<282::AID-PROT3>3.3.CO;2-6

Proteins 36:282-294 (1999)

PubMed id: 10409822

X-ray crystallographic studies of the denaturation of ribonuclease S.

G.S.Ratnaparkhi, R.Varadarajan.

ABSTRACT

In an attempt to view the onset of urea denaturation in ribonuclease we have collected X-ray diffraction data on ribonuclease S crystals soaked in 0, 1.5, 2, 3, and 5 molar urea. At concentrations above 2 M urea, crystals were stabilized by glutaraldehyde crosslinking. We have also collected data on ribonuclease S crystals at low pH in an attempt to study the onset of pH denaturation. The resolution of the datasets range from 1.9 to 3.0 A. Analysis of the structures reveals an increase in disorder with increasing urea concentration. In the 5 M urea structure, this increase in disorder is apparent all over the structure but is larger in loop and helical regions than in the beta strands. The low pH structure shows a very similar pattern of increased disorder. In addition there is a major change in the position of the main chain (> 1 A) in the 65-72 turn region. This region has previously been shown to be involved in one of the initial steps of unfolding in the reduction of ribonuclease A. Crystallographic analyses in the presence of denaturant, when combined with controlled crosslinking, can thus provide detailed structural information that is related to the initial steps of unfolding in solution. Proteins 1999;36:282-294.

Selected figure(s)

Figure 5.
Figure 5. Analysis of water in the high resolution structures. A: RMSD plot. B: B-factor plot.

Figure 6.
Figure 6. Ribbon diagram of RNase S coloured according to value of B factor of the main-chain atoms for (A) 5 M and (B) pH 2* structure. Regions of high, intermediate and low B (Å^2) are colored red, white, and blue respectively (scale inset). The figure was generated using the program INSIGHT-II.

The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (1999, 36, 282-294) copyright 1999.

Figures were selected by an automated process.