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Overview for MACiE Entry M0163

Version history

General Information

EC Number: 3.1.26.4 (A member of the Hydrolases, Acting on ester bonds, Endoribonucleases producing 5'-phosphomonoesters)

Enzyme Name: calf thymus ribonuclease H

Biological Species: Escherichia coli (Bacteria)

Catalytic Chain UniprotKB Accession Codes:

Representative PDB Code: 1rdd - CRYSTAL STRUCTURE OF ESCHERICHIA COLI RNASE HI IN COMPLEXWITH MG2+ AT 2.8 ANGSTROMS RESOLUTION: PROOF FOR A SINGLEMG2+ SITE (Resolution = 2.80 Å).

Catalytic CATH Codes:

Display structure information

Overall Reaction:

Image of RNA

Image of water

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Image of RNA 5-phosphate

Image of RNA 3-hydroxyl

RNA
C00046
CHEBI:33699
water
C00001
CHEBI:15377
RNA 5-phosphate
X00070
RNA 3-hydroxyl
X00069

Overall Comment: Two alternative mechanisms have been proposed for this enzyme. One is a two-metal-ion mechanism where one of the two metal ions activates the attacking hydroxide ion and the other is a general acid-base mechanism where an amino acid residue fulfils this role. NMR and kinetic studies suggest only one metal binds to this protein and that the protein is inactivated by subsequent metal binding events. This makes the general acid base mechanism more plausible [1]. Asp134 holds the nucleophilic water molecule, Glu48 anchors the water molecule that acts as a general acid.


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Stepwise Description of the Reaction

Step 1His124 deprotonates water, which attacks the phosphate of RNA in a nucleophilic substitution that results in the cleavage of the phosphate bond, the 5' end of the RNA molecule reprotonates from magnesium activated water.
Step 2Water deprotonates His124, regenerating the enzyme active site.

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Catalytic Residues Involved

Type Number Chain Location of Function
His 124 A Side Chain

Metal Cofactors for M0163

Type Het group Number Chain
magnesium MG 300 x Overview

References

  1. M. Haruki et al. (2000), Biochemistry, 39, 13939-13944. Catalysis by Escherichia coli ribonuclease HI is facilitated by a phosphate group of the substrate.
    Medline: 11076536
  2. M. Nowotny et al. (2005), Cell, 121, 1005-1016. Crystal structures of RNase H bound to an RNA/DNA hybrid: substrate specificity and metal-dependent catalysis.
    Medline: 15989951

Homologue information for M0163 (1rdd)

CSA Homologues

MACiE Homologues (within the PDB)

MACiE Homologues (within UniprotKB/SwissProt)


Links to this entry in other databases

Link to EC-PDB-SUM Link to PDB-SUM Link to RCSB PDB Link to PDBe Link to CSA
Link to MetaCyc Link to KEGG Link to BRENDA Link to ExplorENZ

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nucleic acid binding (molecular function)
RNA-DNA hybrid ribonuclease activity (molecular function)
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