PDBsum entry: 1yyw

Hydrolase/RNA

PDB-id: 1yyw

Asymmetric unit

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Description

Header details

Header records

References

PROCHECK

Protein chains

219 a.a. *

DNA/RNA

Waters ×94

* Residue conservation analysis

Tools

Clefts Calculation

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

PDB id:

1yyw

Name:

Hydrolase/RNA

Title:

Crystal structure of rnase iii from aquifex aeolicus complexed with double stranded RNA at 2.8-angstrom resolution

Structure:

5'-r( Ap Ap Ap Up Ap Up Ap Up Ap Up Up U)-3'. Chain: e, f, g, h, i, j, k, l. Engineered: yes. Ribonuclease iii. Chain: a, b, c, d. Synonym: rnase iii. Engineered: yes

Source:

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

Biological unit:

Hexamer (from PQS)

UniProt:

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

Seq:

221 a.a.

Struc:

219 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:

2.80Å

R-factor:

0.243

R-free:

0.314

Authors:

J.Gan,J.E.Tropea,B.P.Austin,D.L.Court,D.S.Waugh,X.Ji

Key ref:

J.Gan et al. (2005). Intermediate states of ribonuclease III in complex with double-stranded RNA.. Structure, 13, 1435-1442. [PubMed id: 16216575] [DOI: 10.1016/j.str.2005.06.014]

Date:

25-Feb-05

Release date:

22-Nov-05

Related entries:

1i4s
the crystal structure of rnase iii endonuclease domain from
aquifex aeolicus
1jfz
crystal structure of a mn(ii)complex of rnase iii
endonuclease domain from aquifex aeolicus
1o0w
the crystal structure of rnase iii from thermotoga maritima
1rc5
the crystal structure of a mg(ii) complex of rnase iii
... plus others (see Header records)

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Key reference

DOI no: 10.1016/j.str.2005.06.014

Structure 13:1435-1442 (2005)

PubMed id: 16216575

Intermediate states of ribonuclease III in complex with double-stranded RNA.

J.Gan, J.E.Tropea, B.P.Austin, D.L.Court, D.S.Waugh, X.Ji.

ABSTRACT

Bacterial ribonuclease III (RNase III) can affect RNA structure and gene expression in either of two ways: as a processing enzyme that cleaves double-stranded (ds) RNA, or as a binding protein that binds but does not cleave dsRNA. We previously proposed a model of the catalytic complex of RNase III with dsRNA based on three crystal structures, including the endonuclease domain of RNase III with and without bound metal ions and a dsRNA binding protein complexed with dsRNA. We also reported a noncatalytic assembly observed in the crystal structure of an RNase III mutant, which binds but does not cleave dsRNA, complexed with dsRNA. We hypothesize that the RNase III*dsRNA complex can exist in two functional forms, a catalytic complex and a noncatalytic assembly, and that in between the two forms there may be intermediate states. Here, we present four crystal structures of RNase III complexed with dsRNA, representing possible intermediates.

Selected figure(s)

Figure 4.
Figure 4. Hypothetic Pathways Leading to Two Functional Forms of the RNase III o dsRNA Complex
Six distinct states, conformations A-F, in the pathways are represented by (A) ligand-free Tm-RNase III (PDB code 1O0w), (B) Aa-E110Q o 2-2 (this work), (C) Aa-RNase III o 3-3 (this work), (D) RNA-processing form of Aa-RNase III o dsRNA (this work), (E) Aa-RNase III o 4-4 and Aa-E110K o 4-4 (this work), and (F) noncatalytic form of Aa-E110K o 1-1 (Blaszczyk et al., 2004). The endoND is illustrated as a molecular surface with positive and negative potentials indicated by blue and red colors, respectively; the dsRBD is shown as a Ca backbone worm in white; and the dsRNA is represented as stick models in the atomic color scheme (carbon in white, nitrogen in blue, oxygen in red, and phosphorus in yellow). The circles indicate a possible rotation of the dsRBD o dsRNA moiety enabled by the flexible linker between the endoND and dsRBD; the direction of predicted rotation is indicated by arrowheads on the circles. The figure was created with GRASP (Nicholls et al., 1991). The orientation of the endoND moiety was kept constant.

The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1435-1442) copyright 2005.

Figure was selected by the author.