2E4L

Thermodynamic and Structural Analysis of Thermolabile RNase HI from Shewanella oneidensis MR-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI.

Tadokoro, T.You, D.J.Abe, Y.Chon, H.Matsumura, H.Koga, Y.Takano, K.Kanaya, S.

(2007) Biochemistry 46: 7460-7468

  • DOI: https://doi.org/10.1021/bi7001423
  • Primary Citation of Related Structures:  
    2E4L

  • PubMed Abstract: 

    Ribonuclease (RNase) HI from the psychrotrophic bacterium Shewanella oneidensis MR-1 was overproduced in Escherichia coli, purified, and structurally and biochemically characterized. The amino acid sequence of MR-1 RNase HI is 67% identical to that of E. coli RNase HI. The crystal structure of MR-1 RNase HI determined at 2.0 A resolution was highly similar to that of E. coli RNase HI, except that the number of intramolecular ion pairs and the fraction of polar surface area of MR-1 RNase HI were reduced compared to those of E. coli RNase HI. The enzymatic properties of MR-1 RNase HI were similar to those of E. coli RNase HI. However, MR-1 RNase HI was much less stable than E. coli RNase HI. The stability of MR-1 RNase HI against heat inactivation was lower than that of E. coli RNase HI by 19 degrees C. The conformational stability of MR-1 RNase HI was thermodynamically analyzed by monitoring the CD values at 220 nm. MR-1 RNase HI was less stable than E. coli RNase HI by 22.4 degrees C in Tm and 12.5 kJ/mol in DeltaG(H2O). The thermodynamic stability curve of MR-1 RNase HI was characterized by a downward shift and increased curvature, which results in an increased DeltaCp value, compared to that of E. coli RNase HI. Site-directed mutagenesis studies suggest that the difference in the number of intramolecular ion pairs partly accounts for the difference in stability between MR-1 and E. coli RNases HI.


  • Organizational Affiliation

    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ribonuclease HI158Shewanella oneidensis MR-1Mutation(s): 0 
Gene Names: rnhA
EC: 3.1.26.4
UniProt
Find proteins for Q8EE30 (Shewanella oneidensis (strain ATCC 700550 / JCM 31522 / CIP 106686 / LMG 19005 / NCIMB 14063 / MR-1))
Explore Q8EE30 
Go to UniProtKB:  Q8EE30
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8EE30
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.190 
  • Space Group: P 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.128α = 90
b = 77.128β = 90
c = 76.661γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description