3AA2

A52I E. coli RNase HI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Protein core adaptability: crystal structures of the cavity-filling variants of Escherichia coli RNase HI

Tanaka, M., Chon, H., Angkawidjaja, C., Koga, Y., Takano, K., Kanaya, S.

(2010) Protein Pept.Lett. 17: 1163-1169

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • It has generally been accepted that an increase in protein stability is proportional to the increase in hydrophobicity. When a cavity is created by large-to-small substitutions of amino acid residues in protein cores, protein stability decreases 5.3 ...

    It has generally been accepted that an increase in protein stability is proportional to the increase in hydrophobicity. When a cavity is created by large-to-small substitutions of amino acid residues in protein cores, protein stability decreases 5.3 kJ/mol per single methyl(ene) group removal. In contrast, many reported cavity-filling mutations either failed to increase stability or produced marginal increases in stability; even in successful cases, the increase in stability was much lower than expected from the cost of single methyl(ene) group removal in cavity-creating mutations. Previously it was found that some cavity-filling mutant proteins at Ala52 in E. coli RNase HI increased stability, but decreased activity and they did not increase the stability to the degree expected by the hydrophobic effect alone. The present study attempted to structurally analyze these variant proteins, and it was found that substitutions have little effect on the overall fold but cause conformational strains with the neighboring residues. The present results and literature on cavity-creating/-filling variants provide insight into protein architecture, indicating that natural protein cores are able to accommodate larger side-chain residue by substitution; in other words, excess-packing may not be chosen in natural selection.

    Organizational Affiliation: 

    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease HI
A
155Escherichia coli (strain K12)Mutation(s): 1 
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: 1.9 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.201 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.368α = 90.00
b = 85.301β = 90.00
c = 36.253γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling
HKL-2000data collection
REFMACrefinement

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-11-11 
  • Released Date: 2010-10-06 
  • Deposition Author(s): Takano, K.

Revision History 

  • Version 1.0: 2010-10-06
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance