PDBsum entry 1yyk

Hydrolase/RNA

PDB id

1yyk

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Contents

			Protein chains

					221 a.a. *

			DNA/RNA

			Ligands

					TRS

			Waters ×188

* Residue conservation analysis

PDB id:

1yyk

Links

Name:

Hydrolase/RNA

Title:

Crystal structure of rnase iii from aquifex aeolicus complexed with double-stranded RNA at 2.5-angstrom resolution

Structure:

5'-r( Cp Gp Cp Gp Ap Ap Up Up Cp Gp Cp G)-3'. Chain: c, d, e, f. 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.

Biol. unit:

Hexamer (from PQS)

Resolution:

2.50Å

R-factor:

0.226

R-free:

0.296

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

PROCHECK

	Headers

	References

Protein chains

O67082 (RNC_AQUAE) - Ribonuclease 3 from Aquifex aeolicus (strain VF5)

Seq: Struc:					221 a.a. 221 a.a.

Key:

PfamA domain

Secondary structure

CATH domain

DNA/RNA chains

		C-G-C-G-A-A-U-U-C-G-C-G 12 bases
		C-G-C-G-A-A-U-U-C-G-C-G 12 bases
		C-G-C-G-A-A-U-U-C-G-C-G 12 bases
		C-G-C-G-A-A-U-U-C-G-C-G 12 bases



		Enzyme reactions

Enzyme class:

E.C.3.1.26.3 - ribonuclease Iii.

[IntEnz] [ExPASy] [KEGG] [BRENDA]

Reaction:

Endonucleolytic cleavage to 5'-phosphomonoester.

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.

Figure was selected by the author.

Literature references that cite this PDB file's key reference

PubMed id

Reference

21134127

A.Bekesi, M.Pukancsik, P.Haasz, L.Felfoldi, I.Leveles, V.Muha, E.Hunyadi-Gulyas, A.Erdei, K.F.Medzihradszky, and B.G.Vertessy (2011).
Association of RNA with the uracil-DNA-degrading factor has major conformational effects and is potentially involved in protein folding.

FEBS J, 278, 295-315.

18996395

D.R.Weiss, and M.Levitt (2009).
Can morphing methods predict intermediate structures?

J Mol Biol, 385, 665-674.

18158302

P.Comella, F.Pontvianne, S.Lahmy, F.Vignols, N.Barbezier, A.Debures, E.Jobet, E.Brugidou, M.Echeverria, and J.Sáez-Vásquez (2008).
Characterization of a ribonuclease III-like protein required for cleavage of the pre-rRNA in the 3'ETS in Arabidopsis.

Nucleic Acids Res, 36, 1163-1175.

17194582

I.J.MacRae, and J.A.Doudna (2007).
Ribonuclease revisited: structural insights into ribonuclease III family enzymes.

Curr Opin Struct Biol, 17, 138-145.

16439209

J.Gan, J.E.Tropea, B.P.Austin, D.L.Court, D.S.Waugh, and X.Ji (2006).
Structural insight into the mechanism of double-stranded RNA processing by ribonuclease III.

Cell, 124, 355-366.

PDB code:

2ez6

16855311

X.Ji (2006).
Structural basis for non-catalytic and catalytic activities of ribonuclease III.

Acta Crystallogr D Biol Crystallogr, 62, 933-940.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

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