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Isomerase/structural protein PDB id
2aus
Jmol
Contents
Protein chains
311 a.a. *
53 a.a. *
Ligands
PO4 ×5
Metals
_ZN ×2
Waters ×250
* Residue conservation analysis
PDB id:
2aus
Name: Isomerase/structural protein
Title: Crystal structure of the archaeal box h/aca srnp nop10-cbf5
Structure: Pseudouridine synthase. Chain: c, a. Synonym: probable tRNA pseudouridine synthase b, cbf5, tRNA pseudouridine 55 synthase, psi55 synthase, tRNA-uridine iso tRNA pseudouridylate synthase. Engineered: yes. Ribosome biogenesis protein nop10. Chain: d, b. Synonym: nop10.
Source: Pyrococcus abyssi. Organism_taxid: 29292. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PDB file)
Resolution:
2.10Å     R-factor:   0.224     R-free:   0.252
Authors: C.Charron,X.Manival,B.Charpentier,J.-B.Fourmann,F.Godard,C.B
Key ref: X.Manival et al. (2006). Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity. Nucleic Acids Res, 34, 826-839. PubMed id: 16456033 DOI: 10.1093/nar/gkj482
Date:
29-Aug-05     Release date:   11-Jul-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9V1A5  (TRUB_PYRAB) -  Probable tRNA pseudouridine synthase B
Seq:
Struc: 		334 a.a.
311 a.a.
Protein chains
Pfam   ArchSchema ?
Q9V0E3  (NOP10_PYRAB) -  Ribosome biogenesis protein Nop10
Seq:
Struc: 		60 a.a.
53 a.a.
Key:    PfamA domain  Secondary structure

 Enzyme reactions 
   Enzyme class: Chains C, A: E.C.5.4.99.25  - tRNA pseudouridine(55) synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: tRNA uridine55 = tRNA pseudouridine55
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     ribonucleoprotein complex   1 term 
  Biological process     ribosome biogenesis   6 terms 
  Biochemical function     isomerase activity     3 terms  

 

 
DOI no: 10.1093/nar/gkj482 Nucleic Acids Res 34:826-839 (2006)
PubMed id: 16456033  
 
 
Crystal structure determination and site-directed mutagenesis of the Pyrococcus abyssi aCBF5-aNOP10 complex reveal crucial roles of the C-terminal domains of both proteins in H/ACA sRNP activity.
X.Manival, C.Charron, J.B.Fourmann, F.Godard, B.Charpentier, C.Branlant.
 
  ABSTRACT  
 
In archaeal rRNAs, the isomerization of uridine into pseudouridine (Psi) is achieved by the H/ACA sRNPs and the minimal set of proteins required for RNA:Psi-synthase activity is the aCBF5-aNOP10 protein pair. The crystal structure of the aCBF5-aNOP10 heterodimer from Pyrococcus abyssi was solved at 2.1 A resolution. In this structure, protein aNOP10 has an extended shape, with a zinc-binding motif at the N-terminus and an alpha-helix at the C-terminus. Both motifs contact the aCBF5 catalytic domain. Although less efficiently as does the full-length aNOP10, the aNOP10 C-terminal domain binds aCBF5 and stimulates the RNA-guided activity. We show that the C-terminal domain of aCBF5 (the PUA domain), which is wrapped by an N-terminal extension of aCBF5, plays a crucial role for aCBF5 binding to the guide sRNA. Addition of this domain in trans partially complement particles assembled with an aCBF5DeltaPUA truncated protein. In the crystal structure, the aCBF5-aNOP10 complex forms two kinds of heterotetramers with parallel and perpendicular orientations of the aNOP10 terminal alpha-helices, respectively. By gel filtration assay, we showed that aNOP10 can dimerize in solution. As both residues Y41 and L48 were needed for dimerization, the dimerization likely takes place by interaction of parallel alpha-helices.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21108865 B.Liang, and H.Li (2011).
Structures of ribonucleoprotein particle modification enzymes.
  Q Rev Biophys, 44, 95.  
  21258621 M.A.Trudeau, and J.M.Wong (2010).
Genetic Variations in Telomere Maintenance, with Implications on Tissue Renewal Capacity and Chronic Disease Pathologies.
  Curr Pharmacogenomics Person Med, 8, 7.  
19917616 T.Hamma, and A.R.Ferré-D'Amaré (2010).
The box H/ACA ribonucleoprotein complex: interplay of RNA and protein structures in post-transcriptional RNA modification.
  J Biol Chem, 285, 805-809.  
20227365 T.Kiss, E.Fayet-Lebaron, and B.E.Jády (2010).
Box H/ACA small ribonucleoproteins.
  Mol Cell, 37, 597-606.  
19478803 B.Liang, J.Zhou, E.Kahen, R.M.Terns, M.P.Terns, and H.Li (2009).
Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA.
  Nat Struct Mol Biol, 16, 740-746.
PDB codes: 3hjw 3hjy
19729310 J.Berthon, R.Fujikane, and P.Forterre (2009).
When DNA replication and protein synthesis come together.
  Trends Biochem Sci, 34, 429-434.  
19383767 P.N.Grozdanov, S.Roy, N.Kittur, and U.T.Meier (2009).
SHQ1 is required prior to NAF1 for assembly of H/ACA small nucleolar and telomerase RNPs.
  RNA, 15, 1188-1197.  
18755842 B.Liang, E.J.Kahen, K.Calvin, J.Zhou, M.Blanco, and H.Li (2008).
Long-distance placement of substrate RNA by H/ACA proteins.
  RNA, 14, 2086-2094.  
18178425 H.Li (2008).
Unveiling substrate RNA binding to H/ACA RNPs: one side fits all.
  Curr Opin Struct Biol, 18, 78-85.  
19829749 J.Karijolich, and Y.T.Yu (2008).
Insight into the Protein Components of the Box H/ACA RNP.
  Curr Proteomics, 5, 129-137.  
18539024 R.Ishitani, S.Yokoyama, and O.Nureki (2008).
Structure, dynamics, and function of RNA modification enzymes.
  Curr Opin Struct Biol, 18, 330-339.  
18304947 S.Muller, F.Leclerc, I.Behm-Ansmant, J.B.Fourmann, B.Charpentier, and C.Branlant (2008).
Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in ribosomal RNAs.
  Nucleic Acids Res, 36, 2459-2475.  
18332121 W.A.Decatur, and M.N.Schnare (2008).
Different mechanisms for pseudouridine formation in yeast 5S and 5.8S rRNAs.
  Mol Cell Biol, 28, 3089-3100.  
17318225 A.G.Matera, R.M.Terns, and M.P.Terns (2007).
Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs.
  Nat Rev Mol Cell Biol, 8, 209-220.  
17507419 A.J.Walne, T.Vulliamy, A.Marrone, R.Beswick, M.Kirwan, Y.Masunari, F.H.Al-Qurashi, M.Aljurf, and I.Dokal (2007).
Genetic heterogeneity in autosomal recessive dyskeratosis congenita with one subtype due to mutations in the telomerase-associated protein NOP10.
  Hum Mol Genet, 16, 1619-1629.  
17668295 A.Matte, Z.Jia, S.Sunita, J.Sivaraman, and M.Cygler (2007).
Insights into the biology of Escherichia coli through structural proteomics.
  J Struct Funct Genomics, 8, 45-55.  
17466623 H.Jin, J.P.Loria, and P.B.Moore (2007).
Solution structure of an rRNA substrate bound to the pseudouridylation pocket of a box H/ACA snoRNA.
  Mol Cell, 26, 205-215.
PDB codes: 2pcv 2pcw
17412831 H.Wu, and J.Feigon (2007).
H/ACA small nucleolar RNA pseudouridylation pockets bind substrate RNA to form three-way junctions that position the target U for modification.
  Proc Natl Acad Sci U S A, 104, 6655-6660.
PDB code: 2p89
17803682 I.Pérez-Arellano, J.Gallego, and J.Cervera (2007).
The PUA domain - a structural and functional overview.
  FEBS J, 274, 4972-4984.  
17574834 K.Ye (2007).
H/ACA guide RNAs, proteins and complexes.
  Curr Opin Struct Biol, 17, 287-292.  
17284456 S.L.Reichow, T.Hamma, A.R.Ferré-D'Amaré, and G.Varani (2007).
The structure and function of small nucleolar ribonucleoproteins.
  Nucleic Acids Res, 35, 1452-1464.  
17704128 S.Muller, J.B.Fourmann, C.Loegler, B.Charpentier, and C.Branlant (2007).
Identification of determinants in the protein partners aCBF5 and aNOP10 necessary for the tRNA:Psi55-synthase and RNA-guided RNA:Psi-synthase activities.
  Nucleic Acids Res, 35, 5610-5624.  
17328797 S.Riccardo, G.Tortoriello, E.Giordano, M.Turano, and M.Furia (2007).
The coding/non-coding overlapping architecture of the gene encoding the Drosophila pseudouridine synthase.
  BMC Mol Biol, 8, 15.  
16931875 C.Normand, R.Capeyrou, S.Quevillon-Cheruel, A.Mougin, Y.Henry, and M.Caizergues-Ferrer (2006).
Analysis of the binding of the N-terminal conserved domain of yeast Cbf5p to a box H/ACA snoRNA.
  RNA, 12, 1868-1882.  
16943774 L.Li, and K.Ye (2006).
Crystal structure of an H/ACA box ribonucleoprotein particle.
  Nature, 443, 302-307.
PDB code: 2hvy
16920741 M.Roovers, C.Hale, C.Tricot, M.P.Terns, R.M.Terns, H.Grosjean, and L.Droogmans (2006).
Formation of the conserved pseudouridine at position 55 in archaeal tRNA.
  Nucleic Acids Res, 34, 4293-4301.  
17381322 M.Terns, and R.Terns (2006).
Noncoding RNAs of the H/ACA family.
  Cold Spring Harb Symp Quant Biol, 71, 395-405.  
17135485 N.Kittur, X.Darzacq, S.Roy, R.H.Singer, and U.T.Meier (2006).
Dynamic association and localization of human H/ACA RNP proteins.
  RNA, 12, 2057-2062.  
16647858 U.T.Meier (2006).
How a single protein complex accommodates many different H/ACA RNAs.
  Trends Biochem Sci, 31, 311-315.  
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 codes are shown on the right.