PDBsum entry: 1i4s

Hydrolase

PDB id: 1i4s

Contents

Protein chains

147 a.a. *

Waters ×252

* Residue conservation analysis

PDB id:

1i4s

Name:

Hydrolase

Title:

Crystal structure of rnase iii endonuclease domain from aquifex aeolicus at 2.15 angstrom resolution

Structure:

Ribonuclease iii. Chain: a, b. Fragment: n-terminal endonuclease domain. Synonym: rnase iii. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.15Å R-factor: 0.222 R-free: 0.275

Authors:

J.Blaszczyk,X.Ji

Key ref:

J.Blaszczyk et al. (2001). Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage. Structure, 9, 1225-1236. PubMed id: 11738048 DOI: 10.1016/S0969-2126(01)00685-2

Date:

22-Feb-01 Release date: 19-Dec-01

Protein chains

O67082  (RNC_AQUAE) -  Ribonuclease 3

Seq: 221 a.a.

Struc: 147 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.26.3 - Ribonuclease Iii.
• Reaction: Endonucleolytic cleavage to 5'-phosphomonoester.

 Gene Ontology (GO) functional annotation 

• Biological process: RNA processing (2 terms)
• Biochemical function: RNA binding (2 terms)

DOI no: 10.1016/S0969-2126(01)00685-2

Structure 9:1225-1236 (2001)

PubMed id: 11738048

Crystallographic and modeling studies of RNase III suggest a mechanism for double-stranded RNA cleavage.

J.Blaszczyk, J.E.Tropea, M.Bubunenko, K.M.Routzahn, D.S.Waugh, D.L.Court, X.Ji.

ABSTRACT

BACKGROUND: Aquifex aeolicus Ribonuclease III (Aa-RNase III) belongs to the family of Mg(2+)-dependent endonucleases that show specificity for double-stranded RNA (dsRNA). RNase III is conserved in all known bacteria and eukaryotes and has 1-2 copies of a 9-residue consensus sequence, known as the RNase III signature motif. The bacterial RNase III proteins are the simplest, consisting of two domains: an N-terminal endonuclease domain, followed by a double-stranded RNA binding domain (dsRBD). The three-dimensional structure of the dsRBD in Escherichia coli RNase III has been elucidated; no structural information is available for the endonuclease domain of any RNase III. RESULTS: We present the crystal structures of the Aa-RNase III endonuclease domain in its ligand-free form and in complex with Mn(2+). The structures reveal a novel protein fold and suggest a mechanism for dsRNA cleavage. On the basis of structural, genetic, and biological data, we have constructed a hypothetical model of Aa-RNase III in complex with dsRNA and Mg(2+) ion, which provides the first glimpse of RNase III in action. CONCLUSIONS: The functional Aa-RNase III dimer is formed via mainly hydrophobic interactions, including a "ball-and-socket" junction that ensures accurate alignment of the two monomers. The fold of the polypeptide chain and its dimerization create a valley with two compound active centers at each end of the valley. The valley can accommodate a dsRNA substrate. Mn(2+) binding has significant impact on crystal packing, intermolecular interactions, thermal stability, and the formation of two RNA-cutting sites within each compound active center.

Selected figure(s)

Figure 3.
Figure 3. Structure of the Ligand-free Dimer of Aa-RNase III Endonuclease Domain(a) Dimer interface of Aa-RNase III. Molecule A is illustrated as a surface representation with positive and negative potentials indicated by blue and red, respectively. Molecule B is represented as a backbone "worm" with a stick model for the "ball-and-socket" side chains. The secondary structure elements involved in dimerization are identified with green labels. In the upper portion of the illustration, the shape of the "socket" is shown with the stick model of F41 from Molecule B, whereas, in the lower potion, the shape of the "ball" is outlined in the middle of five side chains that form the socket (see text).(b) A ribbon diagram of molecules A (in green) and B (in blue). The secondary structure assignment is shown in molecule A only. Two sets of six active site residues are labeled, including E37, E40, D44, D107, and E110 from one molecule and E64 from the other. Each set forms a compound active center.(c) A surface representation with red and blue indicating negative and positive potentials, respectively. Notice that the valley on the surface of the dimer has one compound active center on each end of the valley. The representations were prepared using MOLSCRIPT [61], GRASP [62], and Raster3D [63].

The above figure is reprinted by permission from Cell Press: Structure (2001, 9, 1225-1236) copyright 2001.

Figure was selected by an automated process.