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PDBsum entry 1z3l

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protein ligands Protein-protein interface(s) links
Hydrolase PDB id
1z3l
Jmol
Contents
Protein chains
15 a.a.
104 a.a. *
Ligands
SO4 ×2
Waters ×63
* Residue conservation analysis
PDB id:
1z3l
Name: Hydrolase
Title: X-ray crystal structure of a mutant ribonuclease s (f8anb)
Structure: Ribonuclease pancreatic, s-peptide. Chain: s. Synonym: rnase 1, rnase a. Engineered: yes. Mutation: yes. Ribonuclease pancreatic, s-protein. Chain: e. Synonym: rnase 1, rnase a. Ec: 3.1.27.5
Source: Synthetic: yes. Other_details: s-peptide containing the mutations was synthesized by solid phase peptide synthesis. Bos taurus. Cattle. Organism_taxid: 9913
Biol. unit: Dimer (from PQS)
Resolution:
1.80Å     R-factor:   0.197     R-free:   0.226
Authors: M.Das,B.Vasudeva Rao,S.Ghosh,R.Varadarajan
Key ref:
M.Das et al. (2005). Attempts to delineate the relative contributions of changes in hydrophobicity and packing to changes in stability of ribonuclease S mutants. Biochemistry, 44, 5923-5930. PubMed id: 15823052 DOI: 10.1021/bi050001+
Date:
14-Mar-05     Release date:   29-Mar-05    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
15 a.a.*
Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
104 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: Chains S, E: E.C.3.1.27.5  - 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: 10.1021/bi050001+ Biochemistry 44:5923-5930 (2005)
PubMed id: 15823052  
 
 
Attempts to delineate the relative contributions of changes in hydrophobicity and packing to changes in stability of ribonuclease S mutants.
M.Das, B.V.Rao, S.Ghosh, R.Varadarajan.
 
  ABSTRACT  
 
While the hydrophobic driving force is thought to be a major contributor to protein stability, it is difficult to experimentally dissect out its contribution to the overall free energy of folding. We have made large to small substitutions of buried hydrophobic residues at positions 8 and 13 in the peptide/protein complex, RNase-S, and have characterized the structures by X-ray crystallography. The thermodynamics of association of these mutant S peptides with S protein was measured in the presence of different concentrations of methanol and ethanol. The reduction in the strength of the hydrophobic driving force in the presence of these organic solvents was estimated from surface-tension data as well as from the dependence of the DeltaC(p) of protein/peptide binding on the alcohol concentration. The data indicated a decrease in the strength of the hydrophobic driving force of about 30-40% over a 0-30% range of the alcohol concentration. We observe that large to small substitutions destabilize the protein. However, the amount of destabilization, relative to the wild type, is independent of the alcohol concentration over the range of alcohol concentrations studied. The data clearly indicate that decreased stability of the mutants is primarily due to the loss of packing interactions rather than a reduced hydrophobic driving force and suggest a value of the hydrophobic driving force of less than 18 cal mol(-)(1) A(2).
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
18315848 A.Madhumalar, D.J.Smith, and C.Verma (2008).
Stability of the core domain of p53: insights from computer simulations.
  BMC Bioinformatics, 9, S17.  
18565758 S.Yin, Y.Xie, and J.A.Loo (2008).
Mass spectrometry of protein-ligand complexes: enhanced gas-phase stability of ribonuclease-nucleotide complexes.
  J Am Soc Mass Spectrom, 19, 1199-1208.  
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