1LAV

STABILIZATION OF ESCHERICHIA COLI RIBONUCLEASE HI BY CAVITY-FILLING MUTATIONS WITHIN A HYDROPHOBIC CORE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Stabilization of Escherichia coli ribonuclease HI by cavity-filling mutations within a hydrophobic core.

Ishikawa, K.Nakamura, H.Morikawa, K.Kanaya, S.

(1993) Biochemistry 32: 6171-6178

  • Primary Citation of Related Structures:  1LAW

  • PubMed Abstract: 
  • The crystal structure of Escherichia coli ribonuclease HI has a cavity near Val-74 within the protein core. In order to fill the cavity space, we constructed two mutant proteins, V74L and V74I, in which Val-74 was replaced with either Leu or Ile, res ...

    The crystal structure of Escherichia coli ribonuclease HI has a cavity near Val-74 within the protein core. In order to fill the cavity space, we constructed two mutant proteins, V74L and V74I, in which Val-74 was replaced with either Leu or Ile, respectively. The mutant proteins are stabilized, as revealed by a 2.1-3.7 degrees C increase in the Tm values, as compared to the wild-type protein at pH values of 3.0 and 5.5. The mutant protein V74A, in which Val-74 is replaced with Ala, was also constructed to analyze the reverse effect. The stability of V74A decreases by 7.6 degrees C at pH 3.0 and 12.7 degrees C at pH 5.5 in Tm as compared to those values for the wild-type protein. None of the three mutations significantly affect the enzymatic activity. The crystal structures of V74L and V74I, determined at 1.8-A resolution, are almost identical to that of the wild-type protein, except for the mutation site. In the two mutant proteins, calculation by the Voronoi procedure shows that the cavity volumes around the individual mutation sites are remarkably reduced as compared to that in the wild-type protein. These results indicate that the introduction of a methylene group into the cavity, without causing steric clash, contributes to an increase in the hydrophobic interaction within the protein core and thereby enhances protein stability. We also discuss the role of the Leu side chain, which can assume many different local conformations on a helix without sacrificing thermostability.


    Related Citations: 
    • Structural Details of Ribonuclease H from Escherichia Coli as Refined at an Atomic Resolution
      Katayanagi, K.,Miyagawa, M.,Matsushima, M.,Ishikawa, M.,Kanaya, S.,Nakamura, H.,Ikehara, M.,Matsuzaki, T.,Morikawa, K.
      (1992) J.Mol.Biol. 223: 1029
    • Structural Study of Mutants of Escherichia Coli Ribonuclease Hi with Enhanced Thermostability
      Ishikawa, K.,Kimura, S.,Kanaya, S.,Morikawa, K.,Nakamura, H.
      (1993) Protein Eng. 6: 85
    • Three-Dimensional Structure of Ribonuclease H from E. Coli
      Katayanagi, K.,Miyagawa, M.,Matsushima, M.,Ishikawa, M.,Kanaya, S.,Ikehara, M.,Matsuzaki, T.,Morikawa, K.
      (1990) Nature 347: 306


    Organizational Affiliation

    Protein Engineering Research Institute, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE H
A
155Escherichia coli (strain K12)Gene Names: rnhA (dasF, herA, rnh, sdrA)
EC: 3.1.26.4
Find proteins for P0A7Y4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A7Y4
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.150α = 90.00
b = 86.930β = 90.00
c = 35.460γ = 90.00
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other