PDBsum entry: 2apo

Isomerase/RNA binding protein

PDB id: 2apo

Contents

Protein chains

304 a.a. *

55 a.a. *

Metals

__K ×2

_ZN

Waters ×175

* Residue conservation analysis

PDB id:

2apo

Name:

Isomerase/RNA binding protein

Title:

Crystal structure of the methanococcus jannaschii cbf5 nop10 complex

Structure:

Probable tRNA pseudouridine synthase b. Chain: a. Synonym: tRNA pseudouridine 55 synthase, psi55 synthase, tRNA-uridine isomerase, tRNA pseudouridylate synthase. Engineered: yes. Ribosome biogenesis protein nop10. Chain: b. Engineered: yes

Source:

Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: trub. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: nop10.

Biol. unit:

Dimer (from PQS)

Resolution:

1.95Å R-factor: 0.202 R-free: 0.230

Authors:

T.Hamma,S.L.Reichow,G.Varani,A.R.Ferre-D'Amare

Key ref:

T.Hamma et al. (2005). The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs. Nat Struct Mol Biol, 12, 1101-1107. PubMed id: 16286935 DOI: 10.1038/nsmb1036

Date:

16-Aug-05 Release date: 15-Nov-05

Protein chain

Q57612  (TRUB_METJA) -  Probable tRNA pseudouridine synthase B

Seq: 336 a.a.

Struc: 304 a.a.

Protein chain

P81303  (NOP10_METJA) -  Ribosome biogenesis protein Nop10

Seq: 60 a.a.

Struc: 55 a.a.

Enzyme reactions

• Enzyme class: Chain A: E.C.5.4.99.25 - tRNA pseudouridine(55) synthase.
• Reaction: tRNA uridine₅₅ = tRNA pseudouridine₅₅

 Gene Ontology (GO) functional annotation 

• Cellular component: ribonucleoprotein complex (1 term)
• Biological process: ribosome biogenesis (6 terms)
• Biochemical function: isomerase activity (3 terms)

DOI no: 10.1038/nsmb1036

Nat Struct Mol Biol 12:1101-1107 (2005)

PubMed id: 16286935

The Cbf5-Nop10 complex is a molecular bracket that organizes box H/ACA RNPs.

T.Hamma, S.L.Reichow, G.Varani, A.R.Ferré-D'Amaré.

ABSTRACT

Box H/ACA ribonucleoprotein particles (RNPs) catalyze RNA pseudouridylation and direct processing of ribosomal RNA, and are essential architectural components of vertebrate telomerases. H/ACA RNPs comprise four proteins and a multihelical RNA. Two proteins, Cbf5 and Nop10, suffice for basal enzymatic activity in an archaeal in vitro system. We now report their cocrystal structure at 1.95-A resolution. We find that archaeal Cbf5 can assemble with yeast Nop10 and with human telomerase RNA, consistent with the high sequence identity of the RNP components between archaea and eukarya. Thus, the Cbf5-Nop10 architecture is phylogenetically conserved. The structure shows how Nop10 buttresses the active site of Cbf5, and it reveals two basic troughs that bidirectionally extend the active site cleft. Mutagenesis results implicate an adjacent basic patch in RNA binding. This tripartite RNA-binding surface may function as a molecular bracket that organizes the multihelical H/ACA and telomerase RNAs.

Selected figure(s)

Figure 3.
Figure 3. Structure of the Cbf5-Nop10 complex. (a) Overall view. In Cbf5, asterisks mark the active site cleft; dots represent a disordered polypeptide loop; the structurally important Motif I18 is green, Motif II and other active site residues are yellow and the PUA domain19 is gray. In Nop10, the zinc ribbon, linker and C-terminal helix segments are red, pink and purple, respectively (aNop10 color-coding is as in Supplementary Fig. 1; aCbf5 color-coding is as in Supplementary Figs. 4 and 5). (b) View rotated 90°. (c) The aCbf5-aNop10 interface. (d) aNop10 stabilizes the active site of aCbf5 by buttressing residues in Motif I (green) of the enzyme. Water molecules are shown as red spheres, hydrogen bonds as arrows. The catalytic aspartate (Asp81) of aCbf5 is in the lower left corner.

Figure 5.
Figure 5. Conserved surfaces of the Cbf5-Nop10 complex interact with H/ACA guide RNA. (a) Electrostatic potential, mapped onto the solvent-accessible surface of the complex. Two prominently basic features are the girdle extending to either side of the active site (asterisk) and a patch at the interface of the main and PUA domains of aCbf5. (b) View rotated 90°. Two acidic patches represent potential binding sites for the strongly basic H/ACA RNP protein Gar1 (refs. 7,14). Gar1 does not directly interact with RNA but binds dyskerin-Nop10 and thus assembles into the RNP15. (c) Sequence conservation of Cbf5 and Nop10 from archaea to eukarya (Supplementary Figs. 1 and 4) mapped onto the molecular surface of aCbf5 and a worm representation of aNop10 (used because a molecular surface or a solvent-accessible surface representation of aNop10 would occlude the protein-protein interface). Dark green, most highly conserved residues; white, nonconserved residues. The aNop10 trough has dimensions appropriate for accommodating A-form RNA (pink) (see Supplementary Fig. 6). (d) View rotated 90°. (e) Results of electrophoretic mobility shift assays comparing binding of wild-type and mutant aCbf5-aNop10 complexes (S) to an archaeal box H/ACA RNA (F). Locations of mutations are indicated in c. Numbers above the lanes denote protein complex concentrations (nM).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2005, 12, 1101-1107) copyright 2005.

Figures were selected by the author.