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PDBsum entry 3fhc
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protein Protein-protein interface(s) links
Transport protein/hydrolase PDB id
3fhc

 

 

 

 

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Contents
Protein chains
381 a.a. *
224 a.a. *
Waters ×86
* Residue conservation analysis
PDB id:
3fhc
Name: Transport protein/hydrolase
Title: Crystal structure of human dbp5 in complex with nup214
Structure: Nuclear pore complex protein nup214. Chain: a. Fragment: nterminal beta propeller, unp residues 1-405. Synonym: nucleoporin 214kda, nup214, nucleoporin nup214, 214 kda nucleoporin, protein can. Engineered: yes. Atp-dependent RNA helicase ddx19b. Chain: b. Fragment: nterminal reca-like domain, unp residues 68-302.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: nup214 (residues 1-405). Expressed in: escherichia coli. Expression_system_taxid: 511693. Gene: dbp5 (residues 68-302).
Resolution:
2.80Å     R-factor:   0.220     R-free:   0.260
Authors: H.Von Moeller,E.Conti
Key ref:
H.von Moeller et al. (2009). The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner. Nat Struct Biol, 16, 247-254. PubMed id: 19219046 DOI: 10.1038/nsmb.1561
Date:
09-Dec-08     Release date:   17-Feb-09    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P35658  (NU214_HUMAN) -  Nuclear pore complex protein Nup214 from Homo sapiens
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		2090 a.a.
381 a.a.
Protein chain
Pfam   ArchSchema ?
Q9UMR2  (DD19B_HUMAN) -  ATP-dependent RNA helicase DDX19B from Homo sapiens
Seq:
Struc: 		479 a.a.
224 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chain B: E.C.3.6.4.13  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate + H+
ATP
 + H2O
 = ADP
 + phosphate
 + H(+)
Molecule diagrams generated from .mol files obtained from the KEGG ftp site

 

 
    reference    
 
 
DOI no: 10.1038/nsmb.1561 Nat Struct Biol 16:247-254 (2009)
PubMed id: 19219046  
 
 
The mRNA export protein DBP5 binds RNA and the cytoplasmic nucleoporin NUP214 in a mutually exclusive manner.
H.von Moeller, C.Basquin, E.Conti.
 
  ABSTRACT  
 
The DEAD-box protein DBP5 is essential for mRNA export in both yeast and humans. It binds RNA and is concentrated and locally activated at the cytoplasmic side of the nuclear pore complex. We have determined the crystal structures of human DBP5 bound to RNA and AMPPNP, and bound to the cytoplasmic nucleoporin NUP214. The structures reveal that binding of DBP5 to nucleic acid and to NUP214 is mutually exclusive. Using in vitro assays, we demonstrate that NUP214 decreases both the RNA binding and ATPase activities of DBP5. The interactions are mediated by conserved residues, implying a conserved recognition mechanism. These results suggest a framework for the consecutive steps leading to the release of mRNA at the final stages of nuclear export. More generally, they provide a paradigm for how binding of regulators can specifically inhibit DEAD-box proteins.
 
  Selected figure(s)  
 
Figure 1.
(a) Schematic representation of the domain organization of DBP5 with the domain boundaries of the protein constructs used in this study. The RecA-like domains are colored blue and the N-terminal region is shown in orange. (b) Protein precipitations with biotinylated single-stranded RNA identify the RNA binding region of human DBP5 for structural studies. Purified proteins were mixed with 5' end–biotinylated 20-mer single-stranded RNA and incubated with or without AMPPNP or ADP, as indicated. Proteins mixtures before (input, 17% of the total) and after coprecipitation (precipitate) were separated on a 15% (w/v) acrylamide SDS-PAGE and visualized using Coomassie stain. The molecular weight standards are shown in lane 1. DBP5 constructs are described in a. NUP214 C corresponds to residues 1–405 (human sequence). (c) Structure of DBP5 N (light blue) bound to AMPPNP (yellow) and single-stranded RNA (black). The magnesium ion at the ATP binding site is shown in magenta. Six ordered nucleotides of a single-stranded poly-U RNA are present in the 2.2-Å resolution structure. The N- and C-terminal residues of DBP5 visible in the electron density are indicated. The N-terminal region of DBP5 (residues 75–92, orange) folds into a short -helix. This and all other ribbon diagrams in the manuscript were generated using PyMol (http://www.pymol.org). 		Figure 3.
(a) Close-up of the region of interaction between the N-terminal RecA-like domain of DBP5 (in blue) and NUP214 (in green) in the DBP5 N C–NUP214 C structure. The residues involved in hydrophobic and electrostatic interactions are highlighted. (b) Protein precipitations by GST pull-downs with DBP5 and NUP214 mutant proteins. The pull-down assays were carried out as described in Figure 2a. The DBP5 D223R, I258A, R259D or R262A mutations of DBP5 impair its interaction with NUP214. NUP214 V353A shows reduced binding to DBP5, whereas NUP214 D359R impairs the interaction.
 
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2009, 16, 247-254) 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
21428949 D.Klostermeier (2011).
Single-molecule FRET reveals nucleotide-driven conformational changes in molecular machines and their link to RNA unwinding and DNA supercoiling.
  Biochem Soc Trans, 39, 611-616.  
20813532 E.Jankowsky (2011).
RNA helicases at work: binding and rearranging.
  Trends Biochem Sci, 36, 19-29.  
21391900 J.Strohmeier, I.Hertel, U.Diederichsen, M.G.Rudolph, and D.Klostermeier (2011).
Changing nucleotide specificity of the DEAD-box helicase Hera abrogates communication between the Q-motif and the P-loop.
  Biol Chem, 392, 357-369.
PDB codes: 3mwj 3mwk 3mwl 3nbf 3nej
21062831 M.Hilbert, F.Kebbel, A.Gubaev, and D.Klostermeier (2011).
eIF4G stimulates the activity of the DEAD box protein eIF4A by a conformational guidance mechanism.
  Nucleic Acids Res, 39, 2260-2270.  
21079985 P.Björk, and L.Wieslander (2011).
Nucleocytoplasmic mRNP export is an integral part of mRNP biogenesis.
  Chromosoma, 120, 23-38.  
21298575 T.Funasaka, and R.W.Wong (2011).
The role of nuclear pore complex in tumor microenvironment and metastasis.
  Cancer Metastasis Rev, 30, 239-251.  
20307546 A.L.Bifano, E.M.Turk, and M.G.Caprara (2010).
Structure-guided mutational analysis of a yeast DEAD-box protein involved in mitochondrial RNA splicing.
  J Mol Biol, 398, 429-443.  
20566885 J.R.Weir, F.Bonneau, J.Hentschel, and E.Conti (2010).
Structural analysis reveals the characteristic features of Mtr4, a DExH helicase involved in nuclear RNA processing and surveillance.
  Proc Natl Acad Sci U S A, 107, 12139-12144.
PDB code: 2xgj
20719516 M.Stewart (2010).
Nuclear export of mRNA.
  Trends Biochem Sci, 35, 609-617.  
20472641 S.Lattmann, B.Giri, J.P.Vaughn, S.A.Akman, and Y.Nagamine (2010).
Role of the amino terminal RHAU-specific motif in the recognition and resolution of guanine quadruplex-RNA by the DEAH-box RNA helicase RHAU.
  Nucleic Acids Res, 38, 6219-6233.  
20498086 Y.Ren, H.S.Seo, G.Blobel, and A.Hoelz (2010).
Structural and functional analysis of the interaction between the nucleoporin Nup98 and the mRNA export factor Rae1.
  Proc Natl Acad Sci U S A, 107, 10406-10411.
PDB code: 3mmy
19474341 A.R.Karow, and D.Klostermeier (2009).
A conformational change in the helicase core is necessary but not sufficient for RNA unwinding by the DEAD box helicase YxiN.
  Nucleic Acids Res, 37, 4464-4471.  
  19652352 M.Del Campo, and A.M.Lambowitz (2009).
Crystallization and preliminary X-ray diffraction of the DEAD-box protein Mss116p complexed with an RNA oligonucleotide and AMP-PNP.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 832-835.  
19748356 M.Del Campo, and A.M.Lambowitz (2009).
Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA.
  Mol Cell, 35, 598-609.
PDB codes: 3i5x 3i5y 3i61 3i62
19710183 M.G.Rudolph, and D.Klostermeier (2009).
The Thermus thermophilus DEAD box helicase Hera contains a modified RNA recognition motif domain loosely connected to the helicase core.
  RNA, 15, 1993-2001.
PDB codes: 3i31 3i32
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.  
19748337 S.G.Brohawn, J.R.Partridge, J.R.Whittle, and T.U.Schwartz (2009).
The nuclear pore complex has entered the atomic age.
  Structure, 17, 1156-1168.  
19494120 S.R.Carmody, and S.R.Wente (2009).
mRNA nuclear export at a glance.
  J Cell Sci, 122, 1933-1937.  
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.

 

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