2RLN

THERMODYNAMIC AND STRUCTURAL CONSEQUENCES OF CHANGING A SULPHUR ATOM TO A METHYLENE GROUP IN THE M13NLE MUTATION IN RIBONUCLEASE S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Thermodynamic and structural consequences of changing a sulfur atom to a methylene group in the M13Nle mutation in ribonuclease-S.

Thomson, J.Ratnaparkhi, G.S.Varadarajan, R.Sturtevant, J.M.Richards, F.M.

(1994) Biochemistry 33: 8587-8593

  • DOI: 10.1021/bi00194a025
  • Structures With Same Primary Citation

  • PubMed 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), ...

    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)


    Related Citations: 
    • Crystallographic Structures of Ribonuclease S Variants with Nonpolar Substitutions at Position 13: Packing and Cavities
      Varadarajan, R., Richards, F.M.
      (1992) Biochemistry 31: 12315
    • Refinement of the Crystal Structure of Ribonuclease S. Comparison with and between the Various Ribonuclease A Structures
      Kim, E.E., Varadarajan, R., Wyckoff, H.W., Richards, F.M.
      (1992) Biochemistry 31: 12304

    Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut 06511.



Macromolecules
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE
S
16N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE S (S-PROTEIN)
E
109Bos taurusMutation(s): 0 
Gene Names: RNASE1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P61823 (Bos taurus)
Go to UniProtKB:  P61823
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
E
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NLE
Query on NLE
S
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Work: 0.174 
  • R-Value Observed: 0.174 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.74α = 90
b = 44.74β = 90
c = 97.35γ = 120
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1994-11-01
    Type: Initial release
  • Version 1.1: 2008-03-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other