PDBsum entry: 1rc5

Hydrolase

PDB-id: 1rc5

Asymmetric unit

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

148 a.a. *

Metal ions

_MG ×4

Waters ×675

* Residue conservation analysis

Tools

Clefts Calculation

Biological unit*, dimer
(*as deduced by PQS)

PDB id:

1rc5

Name:

Hydrolase

Title:

Crystal structure of mg(ii)-complex of rnase iii endonuclease domain from aquifex aeolicus at 2.30 angstrom resolution

Structure:

Ribonuclease iii. Chain: a, b, c, d. Fragment: n-terminal endonuclease domain (residues 1-147). Synonym: rnase iii. Engineered: yes

Source:

Aquifex aeolicus. Organism_taxid: 63363. Gene: rnc, aq_946. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B, C, D: O67082 (RNC_AQUAE)

Seq:

221 a.a.

Struc:

148 a.a.

Key:	PfamA domain
Secondary structure	CATH domain

Enzyme class:

E.C.3.1.26.3   [IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

Reaction:

Endonucleolytic cleavage to 5'-phosphomonoester.

Resolution:

2.30Å

R-factor:

0.215

R-free:

0.255

Authors:

J.Blaszczyk,J.Gan,X.Ji

Key ref:

J.Blaszczyk et al. (2004). Noncatalytic assembly of ribonuclease III with double-stranded RNA.. Structure, 12, 457-466. [PubMed id: 15016361] [DOI: 10.1016/j.str.2004.02.004]

Date:

03-Nov-03

Release date:

30-Mar-04

Related entries:

1i4s
1i4s is the crystal structure of unligated rnase iii
endonuclease domain from aquifex aeolicus
1stu
1stu is the nmr solution structure of a double-stranded RNA
-binding domain from drosophila staufen protein
1di2
1di2 is the crystal structure of a double-stranded RNA-
binding domain from xenopus laevis complexed with double-
stranded RNA
... plus others (see Header records)

Quick_links

Procheck

Surface

Key reference

DOI no: 10.1016/j.str.2004.02.004

Structure 12:457-466 (2004)

PubMed id: 15016361

Noncatalytic assembly of ribonuclease III with double-stranded RNA.

J.Blaszczyk, J.Gan, J.E.Tropea, D.L.Court, D.S.Waugh, X.Ji.

ABSTRACT

Ribonuclease III (RNase III) represents a family of double-stranded RNA (dsRNA) endonucleases. The simplest bacterial enzyme contains an endonuclease domain (endoND) and a dsRNA binding domain (dsRBD). RNase III can affect RNA structure and gene expression in either of two ways: as a dsRNA-processing enzyme that cleaves dsRNA, or as a dsRNA binding protein that binds but does not cleave dsRNA. We previously determined the endoND structure of Aquifex aeolicus RNase III (Aa-RNase III) and modeled a catalytic complex of full-length Aa-RNase III with dsRNA. Here, we present the crystal structure of Aa-RNase III in complex with dsRNA, revealing a noncatalytic assembly. The major differences between the two functional forms of RNase III.dsRNA are the conformation of the protein and the orientation and location of dsRNA. The flexibility of a 7 residue linker between the endoND and dsRBD enables the transition between these two forms.

Selected figure(s)

Figure 3.
Figure 3. Overall Structure of Aa-E110K·dsRNA(A) Illustration of a biological dimer of the Aa-E110K·dsRNA complex. The crystallographically independent molecule and its symmetry mate are indicated by N-C, and N'-C', respectively. Secondary structural elements are labeled for those in dsRBD and a3 in the endoND. The endoND, dsRBD, dsRNA, endoND^sym, dsRBD^sym, and dsRNA^sym are colored yellow, green, green, cyan, blue, and blue, respectively. The RNase III signature motif at the N terminus of a3 is highlighted in red. Helices, b strands and loops are drawn as spirals, arrows, and pipes, respectively.(B) A different view of dimeric Aa-E110K·dsRNA related to the view in (A) by a 90° rotation around the vertical axis.

The above figure is reprinted by permission from Cell Press: Structure (2004, 12, 457-466) copyright 2004.

Figure was selected by the author.