PDBsum entry 3vn5

Hydrolase

PDB id: 3vn5

Contents

Protein chain

255 a.a.

Waters ×103

PDB id:

3vn5

Name:

Hydrolase

Title:

Crystal structure of aquifex aeolicus rnase h3

Structure:

Ribonuclease hiii. Chain: a. Synonym: rnase hiii. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 224324. Strain: vf5. Gene: aq_1768, rnhc. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.98Å R-factor: 0.206 R-free: 0.238

Authors:

N.Jongruja,D.J.You,K.Eiko,C.Angkawidjaja,Y.Koga,K.Takano,S.Kanaya

Key ref:

N.Jongruja et al. (2012). Structure and characterization of RNase H3 from Aquifex aeolicus. Febs J, 279, 2737-2753. PubMed id: 22686566

Date:

22-Dec-11 Release date: 26-Dec-12

Protein chain

O67644  (RNH3_AQUAE) -  Ribonuclease HIII from Aquifex aeolicus (strain VF5)

Seq: 257 a.a.

Struc: 255 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.26.4 - ribonuclease H.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.

Febs J 279:2737-2753 (2012)

PubMed id: 22686566

Structure and characterization of RNase H3 from Aquifex aeolicus.

N.Jongruja, D.J.You, C.Angkawidjaja, E.Kanaya, Y.Koga, S.Kanaya.

ABSTRACT

The crystal structure of ribonuclease H3 from Aquifex aeolicus (Aae-RNase H3) was determined at 2.0 Å resolution. Aae-RNase H3 consists of an N-terminal TATA box-binding protein (TBP)-like domain (N-domain) and a C-terminal RNase H domain (C-domain). The structure of the C-domain highly resembles that of Bacillus stearothermophilus RNase H3 (Bst-RNase H3), except that it contains three disulfide bonds, and the fourth conserved glutamate residue of the Asp-Glu-Asp-Glu active site motif (Glu198) is located far from the active site. These disulfide bonds were shown to contribute to hyper-stabilization of the protein. Non-conserved Glu194 was identified as the fourth active site residue. The structure of the N-domain without the C-domain also highly resembles that of Bst-RNase H3. However, the arrangement of the N-domain relative to the C-domain greatly varies for these proteins because of the difference in the linker size between the domains. The linker of Bst-RNase H3 is relatively long and flexible, while that of Aae-RNase H3 is short and assumes a helix formation. Biochemical characterizations of Aae-RNase H3 and its derivatives without the N- or C-domain or with a mutation in the N-domain indicate that the N-domain of Aae-RNase H3 is important for substrate binding, and uses the flat surface of the β-sheet for substrate binding. However, this surface is located far from the active site and on the opposite side to the active site. We propose that the N-domain of Aae-RNase H3 is required for initial contact with the substrate. The resulting complex may be rearranged such that only the C-domain forms a complex with the substrate.