Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 17.62 kDa 
• Atom Count: 1338 
• Modelled Residue Count: 155 
• Deposited Residue Count: 155 
• Unique protein chains: 1

1RDA

CRYSTAL STRUCTURES OF RIBONUCLEASE HI ACTIVE SITE MUTANTS FROM ESCHERICHIA COLI

• PDB DOI: 10.2210/pdb1RDA/pdb

• Classification: HYDROLASE(ENDORIBONUCLEASE)
• Organism(s): Escherichia coli
• Mutation(s): No 


• Deposited: 1993-06-23 Released: 1993-10-31 
• Deposition Author(s): Katayanagi, K., Morikawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Observed: 0.189 

Literature

Crystal structures of ribonuclease HI active site mutants from Escherichia coli.

Katayanagi, K., Ishikawa, M., Okumura, M., Ariyoshi, M., Kanaya, S., Kawano, Y., Suzuki, M., Tanaka, I., Morikawa, K.

(1993) J Biol Chem 268: 22092-22099

• PubMed: 8408067 
• Primary Citation of Related Structures:  
  1RDA, 1RDB, 1RDC


• PubMed Abstract: 
  

In order to investigate the relationships between the three-dimensional structure and the enzymic activity of E. coli RNase HI, three mutant proteins, which were completely inactivated by the replacements of three functional residues, Asp10 by Asn (D10N), Glu48 by Gln (E48Q), and Asp70 by Asn (D70N), were crystallized. Their three-dimensional structures were determined by x-ray crystallography. Although the entire backbone structures of these mutants were not affected by the replacements, very localized conformational changes were observed around the Mg(2+)-binding site. The substitution of an amide group for a negatively charged carboxyl group in common induces the formation of new hydrogen bond networks, presumably due to the cancellation of repulsive forces between carboxyl side chains with negative charges. These conformational changes can account for the loss of the enzymic activity in the mutants, and suggest a possible role for Mg2+ in the hydrolysis. Since the 3 replaced acidic residues are completely conserved in sequences of reverse transcriptases from retroviruses, including human immunodeficiency virus, the concepts of the catalytic mechanism deduced from this structural analysis can also be applied to RNase H activity in reverse transcriptases.

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Related Citations: 

• Structural Details of Ribonuclease H from Escherichia Coli as Refined to an Atomic Resolution
  Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Nakamura, H., Ikehara, M., Matsuzaki, T., Morikawa, K.
  (1992) J Mol Biol 223: 1029

• Three-Dimensional Structure of Ribonuclease H from E. Coli
  Katayanagi, K., Miyagawa, M., Matsushima, M., Ishikawa, M., Kanaya, S., Ikehara, M., Matsuzaki, T., Morikawa, K.
  (1990) Nature 347: 306

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Organizational Affiliation: 

Protein Engineering Research Institute, Osaka, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE H	A	155	Escherichia coli	Mutation(s): 0  EC: 3.1.26.4
UniProt
Find proteins for P0A7Y4 (Escherichia coli (strain K12)) Explore P0A7Y4  Go to UniProtKB:  P0A7Y4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Observed: 0.189 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.17	α = 90
b = 87.23	β = 90
c = 35.27	γ = 90

Software Package:

Software Name	Purpose
PROLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1993-06-23 
• Released Date: 1993-10-31 
Deposition Author(s): Katayanagi, K., Morikawa, K.

Revision History  

• Version 1.0: 1993-10-31
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other