PDBsum entry: 2nue

Hydrolase/RNA

PDB-id: 2nue

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Description

Header details

Header records

References

PROCHECK

Protein chains

220 a.a. *

DNA/RNA

Waters ×28

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

2nue

Name:

Hydrolase/RNA

Title:

Crystal structure of rnase iii from aquifex aeolicus complexed with ds-RNA at 2.9-angstrom resolution

Structure:

46-mer. Chain: c. Engineered: yes. Ribonuclease iii. Chain: a, b. Synonym: rnase iii. Engineered: yes

Source:

Synthetic: yes. Aquifex aeolicus. Organism_taxid: 63363. Gene: rnc. Expressed in: escherichia coli. Expression_system_taxid: 562.

UniProt:

Chains A, B: O67082 (RNC_AQUAE)

Seq:

221 a.a.

Struc:

220 a.a.

Key:

PfamA domain

Secondary structure

Enzyme class:

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

Reaction:

Endonucleolytic cleavage to 5'-phosphomonoester.

Resolution:

2.90Å

R-factor:

0.238

R-free:

0.275

Authors:

J.H.Gan,G.Shaw,J.E.Tropea,D.S.Waugh,D.L.Court,X.Ji

Key ref:

J.Gan et al. (2007). A stepwise model for double-stranded RNA processing by ribonuclease III.. Mol Microbiol, 67, 143-154. [PubMed id: 18047582]

Date:

09-Nov-06

Release date:

20-Nov-07

Related entries:

1rc7
crystal structure of rnase iii mutant e110k from aquifex
aeolicus complexed with ds-RNA (5'-ggcgcgcgcc-3')
2ez6
crystal structure of rnase iii mutant d44n from aquifex
aeolicus complexed with products at 2.05-angstrom resolutio
1yz9
crystal structure of rnase iii mutant e110q from aquifex
aeolicus complexed with ds-RNA (5'-cgaacuucgcg-3') at 2.1-
angstrom resolution
... plus others (see Header records)

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Procheck

Clefts

Surface

Key reference

Mol Microbiol 67:143-154 (2007)

PubMed id: 18047582

A stepwise model for double-stranded RNA processing by ribonuclease III.

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

ABSTRACT

RNA interference is mediated by small interfering RNAs produced by members of the ribonuclease III (RNase III) family represented by bacterial RNase III and eukaryotic Rnt1p, Drosha and Dicer. For mechanistic studies, bacterial RNase III has been a valuable model system for the family. Previously, we have shown that RNase III uses two catalytic sites to create the 2-nucleotide (nt) 3' overhangs in its products. Here, we present three crystal structures of RNase III in complex with double-stranded RNA, demonstrating how Mg(2+) is essential for the formation of a catalytically competent protein-RNA complex, how the use of two Mg(2+) ions can drive the hydrolysis of each phosphodiester bond, and how conformational changes in both the substrate and the protein are critical elements for assembling the catalytic complex. Moreover, we have modelled a protein-substrate complex and a protein-reaction intermediate (transition state) complex on the basis of the crystal structures. Together, the crystal structures and the models suggest a stepwise mechanism for RNase III to execute the phosphoryl transfer reaction.