spacer
spacer

PDBsum entry 3bbh
Go to PDB code: 
protein ligands Protein-protein interface(s) links
Transferase PDB id
3bbh

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chains
204 a.a. *
Ligands
SFG ×2
GOL ×6
Waters ×193
* Residue conservation analysis
PDB id:
3bbh
Name: Transferase
Title: M. Jannaschii nep1 complexed with sinefungin
Structure: Ribosome biogenesis protein nep1-like. Chain: a, b. Engineered: yes
Source: Methanocaldococcus jannaschii. Organism_taxid: 2190. Gene: nep1. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
Resolution:
2.25Å     R-factor:   0.216     R-free:   0.244
Authors: A.B.Taylor,B.Meyer,B.Z.Leal,P.Kotter,P.J.Hart,K.-D.Entian,J.Wohnert
Key ref: A.B.Taylor et al. (2008). The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site. Nucleic Acids Res, 36, 1542-1554. PubMed id: 18208838
Date:
09-Nov-07     Release date:   05-Feb-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q57977  (NEP1_METJA) -  Ribosomal RNA small subunit methyltransferase Nep1 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)
Seq:
Struc: 		205 a.a.
204 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.1.1.-  - ?????
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

 

 
Nucleic Acids Res 36:1542-1554 (2008)
PubMed id: 18208838  
 
 
The crystal structure of Nep1 reveals an extended SPOUT-class methyltransferase fold and a pre-organized SAM-binding site.
A.B.Taylor, B.Meyer, B.Z.Leal, P.Kötter, V.Schirf, B.Demeler, P.J.Hart, K.D.Entian, J.Wöhnert.
 
  ABSTRACT  
 
Ribosome biogenesis in eukaryotes requires the participation of a large number of ribosome assembly factors. The highly conserved eukaryotic nucleolar protein Nep1 has an essential but unknown function in 18S rRNA processing and ribosome biogenesis. In Saccharomyces cerevisiae the malfunction of a temperature-sensitive Nep1 protein (nep1-1(ts)) was suppressed by the addition of S-adenosylmethionine (SAM). This suggests the participation of Nep1 in a methyltransferase reaction during ribosome biogenesis. In addition, yeast Nep1 binds to a 6-nt RNA-binding motif also found in 18S rRNA and facilitates the incorporation of ribosomal protein Rps19 during the formation of pre-ribosomes. Here, we present the X-ray structure of the Nep1 homolog from the archaebacterium Methanocaldococcus jannaschii in its free form (2.2 A resolution) and bound to the S-adenosylmethionine analog S-adenosylhomocysteine (SAH, 2.15 A resolution) and the antibiotic and general methyltransferase inhibitor sinefungin (2.25 A resolution). The structure reveals a fold which is very similar to the conserved core fold of the SPOUT-class methyltransferases but contains a novel extension of this common core fold. SAH and sinefungin bind to Nep1 at a preformed binding site that is topologically equivalent to the cofactor-binding site in other SPOUT-class methyltransferases. Therefore, our structures together with previous genetic data suggest that Nep1 is a genuine rRNA methyltransferase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20972225 B.Meyer, J.P.Wurm, P.Kötter, M.S.Leisegang, V.Schilling, M.Buchhaupt, M.Held, U.Bahr, M.Karas, A.Heckel, M.T.Bohnsack, J.Wöhnert, and K.D.Entian (2011).
The Bowen-Conradi syndrome protein Nep1 (Emg1) has a dual role in eukaryotic ribosome biogenesis, as an essential assembly factor and in the methylation of {Psi}1191 in yeast 18S rRNA.
  Nucleic Acids Res, 39, 1526-1537.  
21087996 S.R.Thomas, C.A.Keller, A.Szyk, J.R.Cannon, and N.A.Laronde-Leblanc (2011).
Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis.
  Nucleic Acids Res, 39, 2445-2457.
PDB codes: 3o7b 3oii 3oij 3oin
21098051 H.Y.Chen, and Y.A.Yuan (2010).
Crystal structure of Mj1640/DUF358 protein reveals a putative SPOUT-class RNA methyltransferase.
  J Mol Cell Biol, 2, 366-374.
PDB codes: 3ai9 3aia
20047967 J.P.Wurm, B.Meyer, U.Bahr, M.Held, O.Frolow, P.Kötter, J.W.Engels, A.Heckel, M.Karas, K.D.Entian, and J.Wöhnert (2010).
The ribosome assembly factor Nep1 responsible for Bowen-Conradi syndrome is a pseudouridine-N1-specific methyltransferase.
  Nucleic Acids Res, 38, 2387-2398.  
20858271 X.Wu, S.Sandhu, N.Patel, B.Triggs-Raine, and H.Ding (2010).
EMG1 is essential for mouse pre-implantation embryo development.
  BMC Dev Biol, 10, 99.  
19463982 J.Armistead, S.Khatkar, B.Meyer, B.L.Mark, N.Patel, G.Coghlan, R.E.Lamont, S.Liu, J.Wiechert, P.A.Cattini, P.Koetter, K.Wrogemann, C.R.Greenberg, K.D.Entian, T.Zelinski, and B.Triggs-Raine (2009).
Mutation of a gene essential for ribosome biogenesis, EMG1, causes Bowen-Conradi syndrome.
  Am J Hum Genet, 84, 728-739.  
19369248 M.S.Dunstan, P.C.Hang, N.V.Zelinskaya, J.F.Honek, and G.L.Conn (2009).
Structure of the thiostrepton resistance methyltransferase{middle dot}S-Adenosyl-L-methionine complex and its interaction with ribosomal RNA.
  J Biol Chem, 284, 17013-17020.
PDB code: 3gyq
  20582239 T.Petrossian, and S.Clarke (2009).
Bioinformatic Identification of Novel Methyltransferases.
  Epigenomics, 1, 163-175.  
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.

 

spacer
spacer