PDBsum entry 1j82

Go to PDB code: 
protein ligands Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
16 a.a.
101 a.a. *
Waters ×39
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Osmolyte stabilization of rnase
Structure: Ribonuclease pancreatic. Chain: a. Fragment: s peptide. Synonym: rnase s. Engineered: yes. Ribonuclease pancreatic. Chain: b. Fragment: s protein. Synonym: rnase s.
Source: Synthetic: yes. Other_details: this peptide was chemically synthesized. It is naturally found in bos taurus. Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Biol. unit: Dimer (from PQS)
2.30Å     R-factor:   0.189     R-free:   0.256
Authors: G.S.Ratnaparkhi,R.Varadarajan
Key ref:
G.S.Ratnaparkhi and R.Varadarajan (2001). Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states. J Biol Chem, 276, 28789-28798. PubMed id: 11373282 DOI: 10.1074/jbc.M101906200
19-May-01     Release date:   06-Jun-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
16 a.a.*
Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
150 a.a.
101 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: Chains A, B: E.C.  - Pancreatic ribonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      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 
  GO annot!
  Biochemical function     nucleic acid binding     2 terms  


DOI no: 10.1074/jbc.M101906200 J Biol Chem 276:28789-28798 (2001)
PubMed id: 11373282  
Osmolytes stabilize ribonuclease S by stabilizing its fragments S protein and S peptide to compact folding-competent states.
G.S.Ratnaparkhi, R.Varadarajan.
Osmolytes stabilize proteins to thermal and chemical denaturation. We have studied the effects of the osmolytes sarcosine, betaine, trimethylamine-N-oxide, and taurine on the structure and stability of the protein.peptide complex RNase S using x-ray crystallography and titration calorimetry, respectively. The largest degree of stabilization is achieved with 6 m sarcosine, which increases the denaturation temperatures of RNase S and S pro by 24.6 and 17.4 degrees C, respectively, at pH 5 and protects both proteins against tryptic cleavage. Four crystal structures of RNase S in the presence of different osmolytes do not offer any evidence for osmolyte binding to the folded state of the protein or any perturbation in the water structure surrounding the protein. The degree of stabilization in 6 m sarcosine increases with temperature, ranging from -0.52 kcal mol(-1) at 20 degrees C to -5.4 kcal mol(-1) at 60 degrees C. The data support the thesis that osmolytes that stabilize proteins, do so by perturbing unfolded states, which change conformation to a compact, folding competent state in the presence of osmolyte. The increased stabilization thus results from a decrease in conformational entropy of the unfolded state.
  Selected figure(s)  
Figure 3.
Fig. 3. Effect of sarcosine on the tryptic cleavage of S pro. A, tryptic cleavage of S pro in the absence (lanes 1-5) and presence (lanes 6-10) of 6 M sarcosine. The time points are 0, 10, 20, 30, and 60 min for each case. The arrows indicate the intact S pro and a protected fragment (S pro-(38-124)) in the presence of sarcosine. B, the effect of 6 M sarcosine on the cleavage of a fluorescent substrate of trypsin, BMAAC at pH 8 ( squares) and pH 7 (circles). In the presence of 6 M sarcosine (filled symbols), the rate of trypsin cleavage is half of that in its absence. The rate of cleavage of substrate by trypsin is equal in the absence and presence of 6 M sarcosine if twice the concentration of trypsin is used in the presence of 6 M sarcosine. C, potential sites for tryptic cleavage of S pro (indicated by arrows). The shaded residues indicate the fragment protected (S pro-(38-124)) in the presence of sarcosine. The residue numbering is based on the sequence of RNase A.
Figure 4.
Fig. 4. Effect of osmolytes on the crystal structure of RNase S. The background error for r.m.s.d. and B-factor plots was determined by comparison between the control structures obtained in the absence of osmolyte. A, r.m.s.d. plot for all osmolytes. MC and SC r.m.s.d. values are represented by solid and dashed lines, respectively. The large side-chain r.m.s.d. values are generally due to lack of density for side chains on the surface. The structure was superposed on its control structure before calculating the r.m.s.d. B, the restrained B-factor per residue for the control structure was subtracted from the corresponding B-factor of the structure of interest (osmolyte control) to get the B-factor plot. The filled bars indicate the MC B-factors and the lines represent the SC B-factors. The secondary structure representation on top of the panel indicates helices ( circle ), -strand ( ), and loops/turns ( ). C, r.m.s.d.; D, B-factor plot for the crystallographic water molecules surrounding the osmolyte-soaked proteins. The r.m.s.d. and B-factors were calculated as described above.
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2001, 276, 28789-28798) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21079871 R.W.Watkins, U.Arnold, and R.T.Raines (2011).
Ribonuclease S redux.
  Chem Commun (Camb), 47, 973-975.  
20305088 E.Karaca, A.S.Melquiond, Vries, P.L.Kastritis, and A.M.Bonvin (2010).
Building macromolecular assemblies by information-driven docking: introducing the HADDOCK multibody docking server.
  Mol Cell Proteomics, 9, 1784-1794.  
19883599 F.Meersman, D.Bowron, A.K.Soper, and M.H.Koch (2009).
Counteraction of urea by trimethylamine N-oxide is due to direct interaction.
  Biophys J, 97, 2559-2566.  
19255806 H.L.He, X.L.Chen, X.Y.Zhang, C.Y.Sun, B.C.Zou, and Y.Z.Zhang (2009).
Novel use for the osmolyte trimethylamine N-oxide: retaining the psychrophilic characters of cold-adapted protease deseasin MCP-01 and simultaneously improving its thermostability.
  Mar Biotechnol (NY), 11, 710-716.  
19402134 P.H.Yancey, J.Ishikawa, B.Meyer, P.R.Girguis, and R.W.Lee (2009).
Thiotaurine and hypotaurine contents in hydrothermal-vent polychaetes without thiotrophic endosymbionts: correlation With sulfide exposure.
  J Exp Zool Part A Ecol Genet Physiol, 311, 439-447.  
18213692 R.P.Baptista, S.Pedersen, G.J.Cabrita, D.E.Otzen, J.M.Cabral, and E.P.Melo (2008).
Thermodynamics and mechanism of cutinase stabilization by trehalose.
  Biopolymers, 89, 538-547.  
19048361 Z.Saadati, and A.K.Bordbar (2008).
Stability of beta-Lactoglobulin A in the Presence of Sugar Osmolytes Estimated from Their Guanidinium Chloride-Induced Transition Curves.
  Protein J, 27, 455-460.  
16550379 I.Tashima, T.Yoshida, Y.Asada, and T.Ohmachi (2006).
Purification and characterization of a novel L-2-amino-Delta2-thiazoline-4-carboxylic acid hydrolase from Pseudomonas sp. strain ON-4a expressed in E. coli.
  Appl Microbiol Biotechnol, 72, 499-507.  
16679333 S.K.Gerega, and K.M.Downard (2006).
PROXIMO--a new docking algorithm to model protein complexes using data from radical probe mass spectrometry (RP-MS).
  Bioinformatics, 22, 1702-1709.  
16176595 M.F.Roberts (2005).
Organic compatible solutes of halotolerant and halophilic microorganisms.
  Saline Systems, 1, 5.  
16266274 T.B.Eronina, N.A.Chebotareva, and B.I.Kurganov (2005).
Influence of osmolytes on inactivation and aggregation of muscle glycogen phosphorylase b by guanidine hydrochloride. Stimulation of protein aggregation under crowding conditions.
  Biochemistry (Mosc), 70, 1020-1026.  
12138358 I.Hizoh, and C.Haller (2002).
Radiocontrast-induced renal tubular cell apoptosis: hypertonic versus oxidative stress.
  Invest Radiol, 37, 428-434.  
11767949 M.K.Chow, G.L.Devlin, and S.P.Bottomley (2001).
Osmolytes as modulators of conformational changes in serpins.
  Biol Chem, 382, 1593-1599.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.