PDBsum entry: 2nnw

Transferase

PDB id: 2nnw

Contents

Protein chains

350 a.a. *

227 a.a. *

* Residue conservation analysis

PDB id:

2nnw

Name:

Transferase

Title:

Alternative conformations of nop56/58-fibrillarin complex an implication for induced-fit assenly of box c/d rnps

Structure:

Nop5/nop56 related protein. Chain: a, c. Engineered: yes. Fibrillarin-like rrna/tRNA 2'-o-methyltransferase chain: b, d. Engineered: yes

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: flpa. Expression_system_taxid: 562

Resolution:

2.70Å R-factor: 0.234 R-free: 0.265

Authors:

S.Oruganti,Y.Zhang,R.Terns,M.P.Terns,H.Li

Key ref:

S.Oruganti et al. (2007). Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs. J Mol Biol, 371, 1141-1150. PubMed id: 17617422 DOI: 10.1016/j.jmb.2007.06.029

Date:

24-Oct-06 Release date: 21-Aug-07

Protein chains

Q8U4M1  (Q8U4M1_PYRFU) -  NOP5/NOP56 related protein

Seq: 402 a.a.

Struc: 350 a.a.

Protein chains

Q8U4M2  (FLPA_PYRFU) -  Fibrillarin-like rRNA/tRNA 2'-O-methyltransferase

Seq: 227 a.a.

Struc: 227 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: methylation (3 terms)
• Biochemical function: transferase activity (3 terms)

DOI no: 10.1016/j.jmb.2007.06.029

J Mol Biol 371:1141-1150 (2007)

PubMed id: 17617422

Alternative conformations of the archaeal Nop56/58-fibrillarin complex imply flexibility in box C/D RNPs.

S.Oruganti, Y.Zhang, H.Li, H.Robinson, M.P.Terns, R.M.Terns, W.Yang, H.Li.

ABSTRACT

The Nop56/58-fibrillarin heterocomplex is a core protein complex of the box C/D ribonucleoprotein particles that modify and process ribosomal RNAs. The previous crystal structure of the Archaeoglobus fulgidus complex revealed a symmetric dimer of two Nop56/58-fibrillarin complexes linked by the coiled-coil domains of the Nop56/68 proteins. However, because the A. fulgidus Nop56/58 protein lacks some domains found in most other species, it was thought that the bipartite architecture of the heterocomplex was not likely a general phenomenon. Here we report the crystal structure of the Nop56/58-fibrillarin complex bound with methylation cofactor, S-adenosyl-L-methionine from Pyrococcus furiosus, at 2.7 A. The new complex confirms the generality of the previously observed bipartite arrangement. In addition however, the conformation of Nop56/58 in the new structure differs substantially from that in the earlier structure. The distinct conformations of Nop56/58 suggest potential flexibility in Nop56/58. Computational normal mode analysis supports this view. Importantly, fibrillarin is repositioned within the two complexes. We propose that hinge motion within Nop56/58 has important implications for the possibility of simultaneously positioning two catalytic sites at the two target sites of a bipartite box C/D guide RNA.

Selected figure(s)

Figure 1.
Figure 1. Configuration of the components involved in box C/D RNP assembly. The conserved box C/D sequences and the number of nucleotides found in predicted P. furiosus box C/D RNA spacer regions [from http://lowelab.ucsc.edu/snoRNAdb/] are indicated. The cartoon model represents the structure of A. fulgidus Nop56/58–fibrillarin.

Figure 3.
Figure 3. Structure comparison between Pf (yellow) and Af (green) Nop56/58. (a) Superimposition of the Pf Nop56/58 coiled-coil domain with that of Af Nop56/58. The Pf coiled-coil contains a 56 amino acid insertion that does not disrupt coiled-coil dimerization. (b) A view showing the drastically different placement of the N-terminal domains in Pf (yellow) and Af Nop56/58 (green) with respect to the superimposed coiled-coil domains. Black lines and distances show the path connecting the two SAM molecules in each of the complexes. (Note fibrillarin, the Nop56/58 C-terminal domain, and the Pf insertion domain are not depicted. To see fibrillarin in the complex in the same orientation, see Figure 4.) (c) Difference in the pathway between SAM and the conserved C-terminal domain of Nop56/58 (arbitrarily oriented on the strictly conserved GAEK tetrapeptide region) in the two structures. Only the Pf Nop56/58 C-terminal domain is shown.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 371, 1141-1150) copyright 2007.

Figures were selected by an automated process.