PDBsum entry: 3hjw

Isomerase/RNA

PDB id: 3hjw

Contents

Protein chains

327 a.a. *

53 a.a. *

120 a.a. *

DNA/RNA

Metals

_ZN

__K

Waters ×99

* Residue conservation analysis

PDB id:

3hjw

Name:

Isomerase/RNA

Title:

Structure of a functional ribonucleoprotein pseudouridine sy bound to a substrate RNA

Structure:

Pseudouridine synthase cbf5. Chain: a. Synonym: cbf5, tRNA pseudouridine 55 synthase, psi55 syntha uridine isomerase, tRNA pseudouridylate synthase. Engineered: yes. Ribosome biogenesis protein nop10. Chain: b. Engineered: yes. 50s ribosomal protein l7ae.

Source:

Pyrococcus furiosus. Organism_taxid: 2261. Strain: dsm 3638. Gene: pf1785. Expressed in: escherichia coli. Expression_system_taxid: 562. Gene: pf1141. Gene: pf1367, rpl7ae. Synthetic: yes.

Resolution:

2.35Å R-factor: 0.218 R-free: 0.248

Authors:

B.Liang,J.Zhou,E.Kahen,R.M.Terns,M.P.Terns,H.Li

Key ref:

B.Liang et al. (2009). Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA. Nat Struct Biol, 16, 740-746. PubMed id: 19478803 DOI: 10.1038/nsmb.1624

Date:

22-May-09 Release date: 23-Jun-09

Protein chain

Q7LWY0  (TRUB_PYRFU) -  Probable tRNA pseudouridine synthase B

Seq: 340 a.a.

Struc: 327 a.a.

Protein chain

Q8U1R4  (NOP10_PYRFU) -  Ribosome biogenesis protein Nop10

Seq: 60 a.a.

Struc: 53 a.a.

Protein chain

Q8U160  (RL7A_PYRFU) -  50S ribosomal protein L7Ae

Seq: 123 a.a.

Struc: 120 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: intracellular (3 terms)
• Biological process: ribosome biogenesis (6 terms)
• Biochemical function: isomerase activity (4 terms)

DOI no: 10.1038/nsmb.1624

Nat Struct Biol 16:740-746 (2009)

PubMed id: 19478803

Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA.

B.Liang, J.Zhou, E.Kahen, R.M.Terns, M.P.Terns, H.Li.

ABSTRACT

Box H/ACA small nucleolar and Cajal body ribonucleoprotein particles comprise the most complex pseudouridine synthases and are essential for ribosome and spliceosome maturation. The multistep and multicomponent-mediated enzyme mechanism remains only partially understood. Here we report a crystal structure at 2.35 A of a substrate-bound functional archaeal enzyme containing three of the four proteins, Cbf5, Nop10 and L7Ae, and a box H/ACA RNA that reveals detailed information about the protein-only active site. The substrate RNA, containing 5-fluorouridine at the modification position, is fully docked and catalytically rearranged by the enzyme in a manner similar to that seen in two stand-alone pseudouridine synthases. Structural analysis provides a mechanism for plasticity in the diversity of guide RNA sequences used and identifies a substrate-anchoring loop of Cbf5 that also interacts with Gar1 in unliganded structures. Activity analyses of mutated proteins and RNAs support the structural findings and further suggest a role of the Cbf5 loop in regulation of enzyme activity.

Selected figure(s)

Figure 2.
The modified nucleotide f^5ho^6 was superimposed and oriented in the same way for all three structures. f^5ho^6 is shown in red and the surrounding residues are in blue (Cbf5), cyan (TruB) and green (RluA). The structures of TruB–RNA and RluA–RNA complexes are from PDB 1K8W (ref. 46) and 2I82 (ref. 48), respectively.

Figure 3.
(a) Interactions between the substrate RNA (red) and Cbf5 (green). Dashed lines indicate polar atom contacts within 3.4 Å. Red spheres indicate solvent molecules, and the purple sphere indicates bound potassium. (b) Schematic interactions between the guide (yellow) and substrate RNA (red) with Cbf5 (green).

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 740-746) copyright 2009.

Figures were selected by the author.