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protein dna_rna ligands metals Protein-protein interface(s) links
Hydrolase/RNA PDB id
2db3
Jmol
Contents
Protein chains
420 a.a. *
DNA/RNA
Ligands
ANP ×4
Metals
_MG ×4
Waters ×1319
* Residue conservation analysis
PDB id:
2db3
Name: Hydrolase/RNA
Title: Structural basis for RNA unwinding by the dead-box protein drosophila vasa
Structure: 5'-r( Up Up Up Up Up Up Up Up Up U)-3'. Chain: e, f, g, h. Engineered: yes. Atp-dependent RNA helicase vasa. Chain: a, b, c, d. Fragment: residues 200-623. Synonym: vasa protein, antigen mab46f11. Engineered: yes
Source: Synthetic: yes. Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Gene: vasa. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.20Å     R-factor:   0.197     R-free:   0.250
Authors: T.Sengoku,O.Nureki,A.Nakamura,S.Kobayashi,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
T.Sengoku et al. (2006). Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa. Cell, 125, 287-300. PubMed id: 16630817 DOI: 10.1016/j.cell.2006.01.054
Date:
14-Dec-05     Release date:   02-May-06    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P09052  (VASA1_DROME) -  ATP-dependent RNA helicase vasa, isoform A
Seq:
Struc: 		 
Seq:
Struc: 		661 a.a.
420 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure

 Enzyme reactions 
   Enzyme class: E.C.3.6.4.13  - Rna helicase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: ATP + H2O = ADP + phosphate
ATP
 + H(2)O
 =
ADP
Bound ligand (Het Group name = ANP)
matches with 81.00% similarity 		+ 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  

 

 
    reference    
 
 
DOI no: 10.1016/j.cell.2006.01.054 Cell 125:287-300 (2006)
PubMed id: 16630817  
 
 
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
T.Sengoku, O.Nureki, A.Nakamura, S.Kobayashi, S.Yokoyama.
 
  ABSTRACT  
 
DEAD-box RNA helicases, which regulate various processes involving RNA, have two RecA-like domains as a catalytic core to alter higher-order RNA structures. We determined the 2.2 A resolution structure of the core of the Drosophila DEAD-box protein Vasa in complex with a single-stranded RNA and an ATP analog. The ATP analog intensively interacts with both of the domains, thereby bringing them into the closed form, with many interdomain interactions of conserved residues. The bound RNA is sharply bent, avoiding a clash with a conserved alpha helix in the N-terminal domain. This "wedge" helix should disrupt base pairs by bending one of the strands when a duplex is bound. Mutational analyses indicated that the interdomain interactions couple ATP hydrolysis to RNA unwinding, probably through fine positioning of the duplex relative to the wedge helix. This mechanism, which differs from those for canonical translocating helicases, may enable the targeted modulation of intricate RNA structures.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Overall Structure
(A) Front (right) and side (left) views of the Vasa•RNA•AMPPNP complex. The N-terminal domain (NTD), C-terminal domain (CTD), and flanking sequence are colored blue, red, and yellow, respectively. RNA and AMPPNP are shown in a ball-and-stick representation. Mg^2+ is shown in a space-filling representation.
(B) Locations of the conserved motifs. The bound RNA is colored green.
(C) Superimposition of the NTDs of Vasa, eIF4A, MjDEAD, and UAP56. The β sheets are shown in a ribbon representation. Same view as in (A) and (B).
Figure 3.
Figure 3. RNA Binding and Bending
Blue and red characters indicate residues from the NTD and CTD, respectively. Green broken lines indicate interdomain interactions.
(A) Stereo view near the bending point.
(B) Stereo view of the U4-U5 region.
(C) Stereo view of the U2-U3 region.
(D) Schematic representation. Blue and red arrows indicate interactions through the main chains and the side chains of amino acid residues, respectively. Gray boxes indicate base stacking.
(E) Surface representation of the protein near the α7 helix (stereo view). Motif Ib is colored pink. The bound RNA and the modeled straight RNA are colored green and yellow, respectively.
(F) The α7 helix and its equivalents in DEAD-box proteins. The RNA bound to Vasa is colored green.
(G) The α7 helix and its equivalents in various SF2 proteins. The bent RNA bound to Vasa and the straight DNA bound to NS3 are colored green and yellow, respectively.
 
  The above figures are reprinted by permission from Cell Press: Cell (2006, 125, 287-300) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
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  Acta Crystallogr Sect F Struct Biol Cryst Commun, 65, 832-835.  
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Crystallization and preliminary characterization of the Thermus thermophilus RNA helicase Hera C-terminal domain.
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RNA helicase module in an acetyltransferase that modifies a specific tRNA anticodon.
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  Biosci Rep, 29, 339-349.  
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  Structure, 17, 1528-1537.
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Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline.
  Mol Cell, 36, 231-244.  
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Domain-dependent interaction of eukaryotic initiation factor eIF4A for binding to middle and C-terminal domains of eIF4G.
  J Biochem, 146, 359-368.  
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PDB code: 3gfp
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The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA.
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A DExH/D-box protein coordinates the two steps of splicing in a group I intron.
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18573084 A.M.Pyle (2008).
Translocation and unwinding mechanisms of RNA and DNA helicases.
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Towards deciphering the principles underlying an mRNA recognition code.
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Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase.
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Genetic analysis of the Caenorhabditis elegans GLH family of P-granule proteins.
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19008861 D.Luo, T.Xu, R.P.Watson, D.Scherer-Becker, A.Sampath, W.Jahnke, S.S.Yeong, C.H.Wang, S.P.Lim, A.Strongin, S.G.Vasudevan, and J.Lescar (2008).
Insights into RNA unwinding and ATP hydrolysis by the flavivirus NS3 protein.
  EMBO J, 27, 3209-3219.
PDB codes: 2jlq 2jlr 2jls 2jlu 2jlv 2jlw 2jlx 2jly 2jlz
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ATP hydrolysis is required for DEAD-box protein recycling but not for duplex unwinding.
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Function of the C-terminal domain of the DEAD-box protein Mss116p analyzed in vivo and in vitro.
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Structural insights into the exon junction complex.
  Curr Opin Struct Biol, 18, 112-119.  
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Distinct activities of the DExD/H-box splicing factor hUAP56 facilitate stepwise assembly of the spliceosome.
  Genes Dev, 22, 1796-1803.  
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Differential RNA-dependent ATPase activities of four rRNA processing yeast DEAD-box proteins.
  Biochemistry, 47, 12562-12573.  
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Allosteric activation of the ATPase activity of the Escherichia coli RhlB RNA helicase.
  J Biol Chem, 283, 5567-5576.  
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A conserved phenylalanine of motif IV in superfamily 2 helicases is required for cooperative, ATP-dependent binding of RNA substrates in DEAD-box proteins.
  Mol Cell Biol, 28, 3359-3371.  
18096702 J.Bernstein, D.N.Patterson, G.M.Wilson, and E.A.Toth (2008).
Characterization of the essential activities of Saccharomyces cerevisiae Mtr4p, a 3'->5' helicase partner of the nuclear exosome.
  J Biol Chem, 283, 4930-4942.  
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Protein partners of deubiquitinating enzymes.
  Biochem J, 414, 161-175.  
18270573 L.Lindqvist, M.Oberer, M.Reibarkh, R.Cencic, M.E.Bordeleau, E.Vogt, A.Marintchev, J.Tanaka, F.Fagotto, M.Altmann, G.Wagner, and J.Pelletier (2008).
Selective pharmacological targeting of a DEAD box RNA helicase.
  PLoS ONE, 3, e1583.  
17986459 L.M.Elles, and O.C.Uhlenbeck (2008).
Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype.
  Nucleic Acids Res, 36, 41-50.  
18782831 M.H.Linden, R.K.Hartmann, and D.Klostermeier (2008).
The putative RNase P motif in the DEAD box helicase Hera is dispensable for efficient interaction with RNA and helicase activity.
  Nucleic Acids Res, 36, 5800-5811.  
18719248 N.Rozovsky, A.C.Butterworth, and M.J.Moore (2008).
Interactions between eIF4AI and its accessory factors eIF4B and eIF4H.
  RNA, 14, 2136-2148.  
18606994 P.Schütz, M.Bumann, A.E.Oberholzer, C.Bieniossek, H.Trachsel, M.Altmann, and U.Baumann (2008).
Crystal structure of the yeast eIF4A-eIF4G complex: an RNA-helicase controlled by protein-protein interactions.
  Proc Natl Acad Sci U S A, 105, 9564-9569.
PDB codes: 2vso 2vsx
18267970 R.Lewis, H.Dürr, K.P.Hopfner, and J.Michaelis (2008).
Conformational changes of a Swi2/Snf2 ATPase during its mechano-chemical cycle.
  Nucleic Acids Res, 36, 1881-1890.  
18388857 R.Seidel, J.G.Bloom, C.Dekker, and M.D.Szczelkun (2008).
Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I.
  EMBO J, 27, 1388-1398.  
17951299 S.Wang, M.T.Overgaard, Y.Hu, and D.B.McKay (2008).
The Bacillus subtilis RNA helicase YxiN is distended in solution.
  Biophys J, 94, L01-L03.  
18414490 T.M.Lohman, E.J.Tomko, and C.G.Wu (2008).
Non-hexameric DNA helicases and translocases: mechanisms and regulation.
  Nat Rev Mol Cell Biol, 9, 391-401.  
19088196 Y.Chen, J.P.Potratz, P.Tijerina, M.Del Campo, A.M.Lambowitz, and R.Russell (2008).
DEAD-box proteins can completely separate an RNA duplex using a single ATP.
  Proc Natl Acad Sci U S A, 105, 20203-20208.  
17259309 A.M.Turner, C.F.Love, R.W.Alexander, and P.G.Jones (2007).
Mutational analysis of the Escherichia coli DEAD box protein CsdA.
  J Bacteriol, 189, 2769-2776.  
17229151 A.R.Karow, B.Theissen, and D.Klostermeier (2007).
Authentic interdomain communication in an RNA helicase reconstituted by expressed protein ligation of two helicase domains.
  FEBS J, 274, 463-473.  
17081564 C.Halls, S.Mohr, M.Del Campo, Q.Yang, E.Jankowsky, and A.M.Lambowitz (2007).
Involvement of DEAD-box proteins in group I and group II intron splicing. Biochemical characterization of Mss116p, ATP hydrolysis-dependent and -independent mechanisms, and general RNA chaperone activity.
  J Mol Biol, 365, 835-855.  
17084859 D.N.Frick, S.Banik, and R.S.Rypma (2007).
Role of divalent metal cations in ATP hydrolysis catalyzed by the hepatitis C virus NS3 helicase: magnesium provides a bridge for ATP to fuel unwinding.
  J Mol Biol, 365, 1017-1032.  
17574830 E.Jankowsky, and M.E.Fairman (2007).
RNA helicases--one fold for many functions.
  Curr Opin Struct Biol, 17, 316-324.  
17679086 F.Bleichert, and S.J.Baserga (2007).
The long unwinding road of RNA helicases.
  Mol Cell, 27, 339-352.  
17878153 I.D.Kerr, S.Sivakolundu, Z.Li, J.C.Buchsbaum, L.A.Knox, R.Kriwacki, and S.W.White (2007).
Crystallographic and NMR analyses of UvsW and UvsW.1 from bacteriophage T4.
  J Biol Chem, 282, 34392-34400.
PDB codes: 2jpn 2oca
18022369 I.Gelis, A.M.Bonvin, D.Keramisanou, M.Koukaki, G.Gouridis, S.Karamanou, A.Economou, and C.G.Kalodimos (2007).
Structural basis for signal-sequence recognition by the translocase motor SecA as determined by NMR.
  Cell, 131, 756-769.
PDB code: 2vda
17311413 J.K.Grohman, M.Del Campo, H.Bhaskaran, P.Tijerina, A.M.Lambowitz, and R.Russell (2007).
Probing the mechanisms of DEAD-box proteins as general RNA chaperones: the C-terminal domain of CYT-19 mediates general recognition of RNA.
  Biochemistry, 46, 3013-3022.  
17562711 J.Shen, L.Zhang, and R.Zhao (2007).
Biochemical characterization of the ATPase and helicase activity of UAP56, an essential pre-mRNA splicing and mRNA export factor.
  J Biol Chem, 282, 22544-22550.  
17558417 K.Büttner, S.Nehring, and K.P.Hopfner (2007).
Structural basis for DNA duplex separation by a superfamily-2 helicase.
  Nat Struct Mol Biol, 14, 647-652.
PDB codes: 2p6r 2p6u
17157498 K.P.Hopfner, and J.Michaelis (2007).
Mechanisms of nucleic acid translocases: lessons from structural biology and single-molecule biophysics.
  Curr Opin Struct Biol, 17, 87-95.  
17227144 L.Muzzolini, F.Beuron, A.Patwardhan, V.Popuri, S.Cui, B.Niccolini, M.Rappas, P.S.Freemont, and A.Vindigni (2007).
Different quaternary structures of human RECQ1 are associated with its dual enzymatic activity.
  PLoS Biol, 5, e20.  
17506634 M.R.Singleton, M.S.Dillingham, and D.B.Wigley (2007).
Structure and mechanism of helicases and nucleic acid translocases.
  Annu Rev Biochem, 76, 23-50.  
17964264 Q.Yang, M.Del Campo, A.M.Lambowitz, and E.Jankowsky (2007).
DEAD-box proteins unwind duplexes by local strand separation.
  Mol Cell, 28, 253-263.  
17878217 R.B.Guo, P.Rigolet, H.Ren, B.Zhang, X.D.Zhang, S.X.Dou, P.Y.Wang, M.Amor-Gueret, and X.G.Xi (2007).
Structural and functional analyses of disease-causing missense mutations in Bloom syndrome protein.
  Nucleic Acids Res, 35, 6297-6310.  
17525736 S.Karamanou, G.Gouridis, E.Papanikou, G.Sianidis, I.Gelis, D.Keramisanou, E.Vrontou, C.G.Kalodimos, and A.Economou (2007).
Preprotein-controlled catalysis in the helicase motor of SecA.
  EMBO J, 26, 2904-2914.  
17656723 S.Myong, M.M.Bruno, A.M.Pyle, and T.Ha (2007).
Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase.
  Science, 317, 513-516.  
17584618 W.K.Low, Y.Dang, S.Bhat, D.Romo, and J.O.Liu (2007).
Substrate-dependent targeting of eukaryotic translation initiation factor 4A by pateamine A: negation of domain-linker regulation of activity.
  Chem Biol, 14, 715-727.  
17159905 Z.Cheng, D.Muhlrad, M.K.Lim, R.Parker, and H.Song (2007).
Structural and functional insights into the human Upf1 helicase core.
  EMBO J, 26, 253-264.
PDB codes: 2gjk 2gk6 2gk7
17188036 A.Solem, N.Zingler, and A.M.Pyle (2006).
A DEAD protein that activates intron self-splicing without unwinding RNA.
  Mol Cell, 24, 611-617.  
16931718 C.B.Andersen, L.Ballut, J.S.Johansen, H.Chamieh, K.H.Nielsen, C.L.Oliveira, J.S.Pedersen, B.Séraphin, H.Le Hir, and G.R.Andersen (2006).
Structure of the exon junction core complex with a trapped DEAD-box ATPase bound to RNA.
  Science, 313, 1968-1972.
PDB codes: 2hxy 2hyi
16923391 F.Bono, J.Ebert, E.Lorentzen, and E.Conti (2006).
The crystal structure of the exon junction complex reveals how it maintains a stable grip on mRNA.
  Cell, 126, 713-725.
PDB codes: 2j0q 2j0s 2j0u
16935875 H.Dürr, A.Flaus, T.Owen-Hughes, and K.P.Hopfner (2006).
Snf2 family ATPases and DExx box helicases: differences and unifying concepts from high-resolution crystal structures.
  Nucleic Acids Res, 34, 4160-4167.  
16935881 I.Iost, and M.Dreyfus (2006).
DEAD-box RNA helicases in Escherichia coli.
  Nucleic Acids Res, 34, 4189-4197.  
  17142894 J.M.Caruthers, Y.Hu, and D.B.McKay (2006).
Structure of the second domain of the Bacillus subtilis DEAD-box RNA helicase YxiN.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1191-1195.
PDB code: 2hjv
16826229 L.F.Cavanaugh, A.G.Palmer, L.M.Gierasch, and J.F.Hunt (2006).
Disorder breathes life into a DEAD motor.
  Nat Struct Mol Biol, 13, 566-569.  
16936318 P.Linder (2006).
Dead-box proteins: a family affair--active and passive players in RNP-remodeling.
  Nucleic Acids Res, 34, 4168-4180.  
16630807 P.Linder, and P.Lasko (2006).
Bent out of shape: RNA unwinding by the DEAD-box helicase Vasa.
  Cell, 125, 219-221.  
17072313 Q.Yang, and E.Jankowsky (2006).
The DEAD-box protein Ded1 unwinds RNA duplexes by a mode distinct from translocating helicases.
  Nat Struct Mol Biol, 13, 981-986.  
16982642 S.D.Auweter, F.C.Oberstrass, and F.H.Allain (2006).
Sequence-specific binding of single-stranded RNA: is there a code for recognition?
  Nucleic Acids Res, 34, 4943-4959.  
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