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PDBsum entry 2rln

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protein ligands Protein-protein interface(s) links
Hydrolase(phosphoric diester,RNA) PDB id
2rln
Jmol
Contents
Protein chains
16 a.a.
104 a.a. *
Ligands
SO4
Waters ×54
* Residue conservation analysis
PDB id:
2rln
Name: Hydrolase(phosphoric diester,RNA)
Title: Thermodynamic and structural consequences of changing a sulphur atom to a methylene group in the m13nle mutation in ribonuclease s
Structure: Ribonuclease. Chain: s. Engineered: yes. Ribonuclease s (s-protein). Chain: e. Engineered: yes
Source: Bos taurus. Cattle. Organism_taxid: 9913. Organ: pancreas
Biol. unit: Dimer (from PQS)
Resolution:
1.85Å     R-factor:   0.174    
Authors: G.Ratnaparkhi,R.Varadarajan
Key ref:
J.Thomson et al. (1994). Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S. Biochemistry, 33, 8587-8593. PubMed id: 8031793 DOI: 10.1021/bi00194a025
Date:
11-Jul-94     Release date:   01-Nov-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P61823  (RNAS1_BOVIN) -  Ribonuclease pancreatic
Seq:
Struc:
150 a.a.
16 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/bi00194a025 Biochemistry 33:8587-8593 (1994)
PubMed id: 8031793  
 
 
Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S.
J.Thomson, G.S.Ratnaparkhi, R.Varadarajan, J.M.Sturtevant, F.M.Richards.
 
  ABSTRACT  
 
Two fragments of pancreatic ribonuclease A, a truncated version of S-peptide (residues 1-15) and S-protein (residues 21-124), combine to give a catalytically active complex. We have substituted the wild-type residue at position 13, methionine (Met), with norleucine (Nle), where the only covalent change is the replacement of the sulfur atom with a methylene group. The thermodynamic parameters associated with the binding of this variant to S-protein, determined by titration calorimetry in the temperature range 10-40 degrees C, are reported and compared to values previously reported [Varadarajan, R., Connelly, P. R., Sturtevant, J. M., & Richards, F. M. (1992) Biochemistry 31, 1421-1426] for other position 13 analogs. The differences in the free energy and enthalpy of binding between the Met and Nle peptides are 0.6 and 7.9 kcal/mol at 25 degrees C, respectively. These differences are slightly larger than, but comparable to, the differences in the values for the Met/Ile and Met/Leu pairs. The structure of the mutant complex was determined to 1.85 A resolution and refined to an R-factor of 17.4%. The structures of mutant and wild-type complexes are practically identical although the Nle side chain has a significantly higher average B-factor than the corresponding Met side chain. In contrast, the B-factors of the atoms of the cage of residues surrounding position 13 are all somewhat lower in the Nle variant than the Met wild-type.(ABSTRACT TRUNCATED AT 250 WORDS)
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21325613 A.Bachmann, D.Wildemann, F.Praetorius, G.Fischer, and T.Kiefhaber (2011).
Mapping backbone and side-chain interactions in the transition state of a coupled protein folding and binding reaction.
  Proc Natl Acad Sci U S A, 108, 3952-3957.  
21079871 R.W.Watkins, U.Arnold, and R.T.Raines (2011).
Ribonuclease S redux.
  Chem Commun (Camb), 47, 973-975.  
20876137 G.Ofek, F.J.Guenaga, W.R.Schief, J.Skinner, D.Baker, R.Wyatt, and P.D.Kwong (2010).
Elicitation of structure-specific antibodies by epitope scaffolds.
  Proc Natl Acad Sci U S A, 107, 17880-17887.
PDB codes: 3les 3lev 3lex 3ley
17868092 G.R.Marshall, J.A.Feng, and D.J.Kuster (2008).
Back to the future: ribonuclease A.
  Biopolymers, 90, 259-277.  
17006876 A.Ababou, and J.E.Ladbury (2007).
Survey of the year 2005: literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 20, 4.  
15465316 J.E.Ladbury, and M.A.Williams (2004).
The extended interface: measuring non-local effects in biomolecular interactions.
  Curr Opin Struct Biol, 14, 562-569.  
14732929 M.J.Cliff, and J.E.Ladbury (2003).
A survey of the year 2002 literature on applications of isothermal titration calorimetry.
  J Mol Recognit, 16, 383-391.  
12070144 S.Chakravarty, A.Bhinge, and R.Varadarajan (2002).
A procedure for detection and quantitation of cavity volumes proteins. Application to measure the strength of the hydrophobic driving force in protein folding.
  J Biol Chem, 277, 31345-31353.  
11015216 G.S.Ratnaparkhi, and R.Varadarajan (2000).
Thermodynamic and structural studies of cavity formation in proteins suggest that loss of packing interactions rather than the hydrophobic effect dominates the observed energetics.
  Biochemistry, 39, 12365-12374.
PDB codes: 1d5d 1d5e 1d5h
10393919 G.Chakshusmathi, G.S.Ratnaparkhi, P.K.Madhu, and R.Varadarajan (1999).
Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments.
  Proc Natl Acad Sci U S A, 96, 7899-7904.  
  10210190 T.Yuan, and H.J.Vogel (1999).
Substitution of the methionine residues of calmodulin with the unnatural amino acid analogs ethionine and norleucine: biochemical and spectroscopic studies.
  Protein Sci, 8, 113-121.  
9521665 C.S.Miles, F.Lederer, and K.H.Lê (1998).
Probing intramolecular electron transfer within flavocytochrome b2 with a monoclonal antibody.
  Biochemistry, 37, 3440-3448.  
8939696 J.E.Ladbury, and B.Z.Chowdhry (1996).
Sensing the heat: the application of isothermal titration calorimetry to thermodynamic studies of biomolecular interactions.
  Chem Biol, 3, 791-801.  
8574705 G.E.Plum, and K.J.Breslauer (1995).
Calorimetry of proteins and nucleic acids.
  Curr Opin Struct Biol, 5, 682-690.  
7765170 P.R.Connelly (1994).
Acquisition and use of calorimetric data for prediction of the thermodynamics of ligand-binding and folding reactions of proteins.
  Curr Opin Biotechnol, 5, 381-388.  
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. Where a reference describes a PDB structure, the PDB codes are shown on the right.