1RIL

CRYSTAL STRUCTURE OF RIBONUCLEASE H FROM THERMUS THERMOPHILUS HB8 REFINED AT 2.8 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of ribonuclease H from Thermus thermophilus HB8 refined at 2.8 A resolution.

Ishikawa, K.Okumura, M.Katayanagi, K.Kimura, S.Kanaya, S.Nakamura, H.Morikawa, K.

(1993) J Mol Biol 230: 529-542

  • DOI: 10.1006/jmbi.1993.1169
  • Primary Citation of Related Structures:  
    1RIL

  • PubMed Abstract: 
  • The crystal structure of Thermus thermophilus RNase H was determined at 2.8 A resolution. The structure was solved by the molecular replacement method, based on the accurately refined structure of Escherichia coli RNase HI, which shows 52% amino acid sequence identity ...

    The crystal structure of Thermus thermophilus RNase H was determined at 2.8 A resolution. The structure was solved by the molecular replacement method, based on the accurately refined structure of Escherichia coli RNase HI, which shows 52% amino acid sequence identity. Crystallographic refinement led to an R-factor of 0.205, with a 0.019 A root-mean-square deviation from ideal bond lengths and 0.048 A from ideal bond angle distances. Structural comparison shows a striking similarity in the overall folding of the thermophilic and mesophilic enzymes. The root-mean-square displacement is 0.95 A between equivalent alpha-carbon atoms from all elements of secondary structure (five alpha-helices and five beta-strands). However, some notable differences, which account for the enhanced thermostability of T. thermophilus RNase H, are observed in loop structures and side-chain conformations. The substitution of Gly for the left-handed helical residue (Lys95) in the E. coli enzyme is proposed to substantially enhance the thermostability, due to the release of steric hindrance caused by the beta-carbon atom. Furthermore, it is likely that the expansion of an aromatic cluster, arising from the replacement of Ile78 in the mesophilic enzyme by Phe, and the increased number of salt-bridges additively contribute to the stability.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of Ribonuclease H from Thermus Thermophilus Hb8
      Okumura, M., Ishikawa, K., Kanaya, S., Itaya, M., Morikawa, K.
      (1993) Proteins 15: 108

    Organizational Affiliation

    Protein Engineering Research Institute, Osaka, Japan.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE HA166Thermus thermophilusMutation(s): 0 
EC: 3.1.26.4
Find proteins for P29253 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Explore P29253 
Go to UniProtKB:  P29253
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Observed: 0.205 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.7α = 90
b = 44.7β = 90
c = 314.7γ = 120
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1993-10-31
    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