PDBsum entry 3fho

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Hydrolase PDB id
Protein chains
305 a.a.
PDB id:
Name: Hydrolase
Title: Structure of s. Pombe dbp5
Structure: Atp-dependent RNA helicase dbp5. Chain: a, b. Engineered: yes
Source: Schizosaccharomyces pombe. Fission yeast. Organism_taxid: 4896. Gene: dbp5. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.80Å     R-factor:   0.292     R-free:   0.327
Authors: Z.Cheng,H.Song
Key ref:
J.S.Fan et al. (2009). Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides. J Mol Biol, 388, 1. PubMed id: 19281819 DOI: 10.1016/j.jmb.2009.03.004
09-Dec-08     Release date:   13-Oct-09    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
Q09747  (DBP5_SCHPO) -  ATP-dependent RNA helicase dbp5
503 a.a.
305 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 6 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
+ H(2)O
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     4 terms  


DOI no: 10.1016/j.jmb.2009.03.004 J Mol Biol 388:1 (2009)
PubMed id: 19281819  
Solution and crystal structures of mRNA exporter Dbp5p and its interaction with nucleotides.
J.S.Fan, Z.Cheng, J.Zhang, C.Noble, Z.Zhou, H.Song, D.Yang.
DEAD-box protein 5 (Dbp5p) plays very important roles in RNA metabolism from transcription, to translation, to RNA decay. It is an RNA helicase and functions as an essential RNA export factor from nucleus. Here, we report the solution NMR structures of the N- and C-terminal domains (NTD and CTD, respectively) of Dbp5p from Saccharomyces cerevisiae (ScDbp5p) and X-ray crystal structure of Dbp5p from Schizosaccharomyces pombe (SpDbp5p) in the absence of nucleotides and RNA. The crystal structure clearly shows that SpDbp5p comprises two RecA-like domains that do not interact with each other. NMR results show that the N-terminal flanking region of ScDpbp5 (M1-E70) is intrinsically unstructured and the region Y71-R121 including the Q motif is highly dynamic on millisecond-microsecond timescales in solution. The C-terminal flanking region of ScDbp5p forms a short beta-strand and a long helix. This helix is unique for ScDbp5p and has not been observed in other DEAD-box proteins. Compared with other DEAD-box proteins, Dbp5p has an extra insert with six residues in the CTD. NMR structure reveals that the insert is located in a solvent-exposed loop capable of interacting with other proteins. ATP and ADP titration experiments show that both ADP and ATP bind to the consensus binding site in the NTD of ScDbp5p but do not interact with the CTD at all. Binding of ATP or ADP to NTD induces significant conformational rearrangement too.
  Selected figure(s)  
Figure 1.
Fig. 1. Stereo views of 20 superimposed accepted structures for NTD and CTD of ScDbp5p. The figure was generated using MOLMOL.^40 Only backbone atoms (N, C^α, C′, and CO) were chosen to superimpose the structures. (a) The region from Q81 to T296 was drawn to represent the NTD structure. (b) The region from T296 to D482 was drawn to represent the CTD structure.
Figure 2.
Fig. 2. NMR and crystal structures of Dbp5p proteins. (a) NMR structure of CTD of ScDbp5p. α-helices and β-strands are colored cyan and magenta, respectively. The extreme C-terminal helix in CTD is shown in red. The first residue number of CTD is 296. (b) NMR structure of NTD of ScDbp5p. The color coding is the same as that in (a) with the exception that the N-terminal extension region is shown in green. (c) Overall structure of SpDbp5p solved by X-ray chromatography. The color coding is the same as that in (a). (d) Stereo view of superposition of SpDbp5p and HuDbp5p-ADP at the NTD. SpDbp5p is colored yellow and HuDbp5p-ADP is in gray, with its N-terminal region in magenta and the bound ADP in stick model. (e) Stereo view of superposition of the NTD of ScDbp5p with that of HuDbp5p-ADP. The N-terminal extension regions with residue numbers from 71 to 100 in ScDbp5p and from 53 to 100 in HuDbp5p are shown in green and magenta, respectively. The positions of residues 71 and 90 are also labeled.
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 388, 1) copyright 2009.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21441902 B.Montpetit, N.D.Thomsen, K.J.Helmke, M.A.Seeliger, J.M.Berger, and K.Weis (2011).
A conserved mechanism of DEAD-box ATPase activation by nucleoporins and InsP6 in mRNA export.
  Nature, 472, 238-242.
PDB codes: 3peu 3pev 3pew 3pex 3pey 3pez 3rrm 3rrn
21779027 P.Linder, and E.Jankowsky (2011).
From unwinding to clamping - the DEAD box RNA helicase family.
  Nat Rev Mol Cell Biol, 12, 505-516.  
20719516 M.Stewart (2010).
Nuclear export of mRNA.
  Trends Biochem Sci, 35, 609-617.  
20471947 R.Perriman, and M.Ares (2010).
Invariant U2 snRNA nucleotides form a stem loop to recognize the intron early in splicing.
  Mol Cell, 38, 416-427.  
19747077 M.Hilbert, A.R.Karow, and D.Klostermeier (2009).
The mechanism of ATP-dependent RNA unwinding by DEAD box proteins.
  Biol Chem, 390, 1237-1250.  
19805289 Z.Y.Dossani, C.S.Weirich, J.P.Erzberger, J.M.Berger, and K.Weis (2009).
Structure of the C-terminus of the mRNA export factor Dbp5 reveals the interaction surface for the ATPase activator Gle1.
  Proc Natl Acad Sci U S A, 106, 16251-16256.
PDB code: 3gfp
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.