1G15

CO-CRYSTAL OF E. COLI RNASE HI WITH TWO MN2+ IONS BOUND IN THE THE ACTIVE SITE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Co-crystal of Escherichia coli RNase HI with Mn2+ ions reveals two divalent metals bound in the active site.

Goedken, E.R.Marqusee, S.

(2001) J.Biol.Chem. 276: 7266-7271

  • DOI: 10.1074/jbc.M009626200

  • PubMed Abstract: 
  • Ribonuclease H (RNase H) selectively degrades the RNA strand of RNA.DNA hybrids in a divalent cation-dependent manner. Previous structural studies revealed a single Mg(2+) ion-binding site in Escherichia coli RNase HI. In the crystal structure of the ...

    Ribonuclease H (RNase H) selectively degrades the RNA strand of RNA.DNA hybrids in a divalent cation-dependent manner. Previous structural studies revealed a single Mg(2+) ion-binding site in Escherichia coli RNase HI. In the crystal structure of the related RNase H domain of human immunodeficiency virus reverse transcriptase, however, two Mn(2+) ions were observed suggesting a different mode of metal binding. E. coli RNase HI shows catalytic activity in the presence of Mg(2+) or Mn(2+) ions, but these two metals show strikingly different optimal concentrations. Mg(2+) ions are required in millimolar concentrations, but Mn(2+) ions are only required in micromolar quantities. Based upon the metal dependence of E. coli RNase HI activity, we proposed an activation/attenuation model in which one metal is required for catalysis, and binding of a second metal is inhibitory. We have now solved the co-crystal structure of E. coli RNase HI with Mn(2+) ions at 1.9-A resolution. Two octahedrally coordinated Mn(2+) ions are seen to bind to the enzyme-active site. Residues Asp-10, Glu-48, and Asp-70 make direct (inner sphere) coordination contacts to the first (activating) metal, whereas residues Asp-10 and Asp-134 make direct contacts to the second (attenuating) metal. This structure is consistent with biochemical evidence suggesting that two metal ions may bind RNase H but liganding a second ion inhibits RNase H activity.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEASE HI
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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.223 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 71.653α = 90.00
b = 71.653β = 90.00
c = 48.127γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
MOSFLMdata reduction
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-03-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance