3H08

Crystal structure of the Ribonuclease H1 from Chlorobium tepidum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure, stability, and folding of ribonuclease H1 from the moderately thermophilic chlorobium tepidum: comparison with thermophilic and mesophilic homologues.

Ratcliff, K.Corn, J.Marqusee, S.

(2009) Biochemistry 48: 5890-5898

  • DOI: 10.1021/bi900305p

  • PubMed Abstract: 
  • Proteins from thermophilic organisms are able to function under conditions that render a typical mesophilic protein inactive. Pairwise comparisons of homologous mesophilic and thermophilic proteins can help to identify the energetic features of a pro ...

    Proteins from thermophilic organisms are able to function under conditions that render a typical mesophilic protein inactive. Pairwise comparisons of homologous mesophilic and thermophilic proteins can help to identify the energetic features of a protein's energy landscape that lead to such thermostability. Previous studies of bacterial ribonucleases H (RNases H) from the thermophile Thermus thermophilus and the mesophile Escherichia coli revealed that the thermostability arises in part from an unusually low change in heat capacity upon unfolding (DeltaC(p)) for the thermophilic protein [Hollien, J., and Marqusee, S. (1999) Biochemistry 38, 3831-3836]. Here, we have further examined how nearly identical proteins can adapt to different thermal constraints by adding a moderately thermophilic homologue to the previously characterized mesophilic and thermophilic pair. We identified a putative RNase H from Chlorobium. tepidum and demonstrated that it is an active RNase H and adopts the RNase H fold. The moderately thermophilic protein has a melting temperature (T(m)) similar to that of the mesophilic homologue yet also has a surprisingly low DeltaC(p), like the thermophilic homologue. This new RNase H folds through a pathway similar to that of the previously studied RNases H. These results suggest that lowering the DeltaC(p) may be a general strategy for achieving thermophilicity for some protein families and implicate the folding core as the major contributor to this effect. It should now be possible to design RNases H that display the desired thermophilic or mesophilic properties, as defined by their DeltaC(p) values, and therefore fine-tune the energy landscape in a predictable fashion.


    Organizational Affiliation

    Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Rnh (Ribonuclease H)
A, B
146Chlorobaculum tepidumMutation(s): 3 
Gene Names: rnh (rnhA)
EC: 3.1.26.4
Find proteins for Q93SU7 (Chlorobaculum tepidum)
Go to UniProtKB:  Q93SU7
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.160 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 33.457α = 100.38
b = 33.388β = 99.43
c = 66.072γ = 90.82
Software Package:
Software NamePurpose
HKL-2000data collection
REFMACrefinement
SOLVEphasing
HKL-2000data scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance