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PDBsum entry 3g0h
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Hydrolase/RNA
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PDB id
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3g0h
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Contents |
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* Residue conservation analysis
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PDB id:
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Hydrolase/RNA
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Title:
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Human dead-box RNA helicase ddx19, in complex with an atp-analogue and RNA
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Structure:
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Atp-dependent RNA helicase ddx19b. Chain: a. Fragment: unp residues 54-275. Synonym: dead box protein 19b, dead box RNA helicase dead5. Engineered: yes. 5'-r(p Up Up Up Up Up Up U)-3'. Chain: e. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Gene: dbp5, ddx19, ddx19b. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes
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Resolution:
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2.70Å
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R-factor:
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0.220
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R-free:
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0.275
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Authors:
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T.Karlberg,L.Lehtio,R.Collins,C.H.Arrowsmith,H.Berglund,C.Bountra, L.G.Dahlgren,A.M.Edwards,S.Flodin,A.Flores,S.Graslund,M.Hammarstrom, A.Johansson,I.Johansson,T.Kotenyova,M.Moche,M.E.Nilsson,P.Nordlund, T.Nyman,C.Persson,J.Sagemark,P.Schutz,M.I.Siponen,A.G.Thorsell, L.Tresaugues,S.Van Den Berg,J.Weigelt,M.Welin,M.Wisniewska, H.Schuler,Structural Genomics Consortium (Sgc)
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Key ref:
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R.Collins
et al.
(2009).
The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch.
J Biol Chem,
284,
10296-10300.
PubMed id:
DOI:
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Date:
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28-Jan-09
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Release date:
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17-Feb-09
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PROCHECK
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Headers
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References
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Q9UMR2
(DD19B_HUMAN) -
ATP-dependent RNA helicase DDX19B from Homo sapiens
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Seq:
Struc:
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479 a.a.
408 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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Enzyme class:
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E.C.3.6.4.13
- Rna helicase.
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Reaction:
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ATP + H2O = ADP + phosphate + H+
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ATP
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+
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H2O
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=
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ADP
Bound ligand (Het Group name = )
matches with 81.25% similarity
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+
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phosphate
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+
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H(+)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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DOI no:
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J Biol Chem
284:10296-10300
(2009)
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PubMed id:
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The DEXD/H-box RNA Helicase DDX19 Is Regulated by an {alpha}-Helical Switch.
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R.Collins,
T.Karlberg,
L.Lehtiö,
P.Schütz,
S.van den Berg,
L.G.Dahlgren,
M.Hammarström,
J.Weigelt,
H.Schüler.
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ABSTRACT
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DEXD/H-box RNA helicases couple ATP hydrolysis to RNA remodeling by an unknown
mechanism. We used x-ray crystallography and biochemical analysis of the human
DEXD/H-box protein DDX19 to investigate its regulatory mechanism. The crystal
structures of DDX19, in its RNA-bound prehydrolysis and free posthydrolysis
state, reveal an alpha-helix that inserts between the conserved domains of the
free protein to negatively regulate ATPase activity. This finding was
corroborated by biochemical data that confirm an autoregulatory function of the
N-terminal region of the protein. This is the first study describing crystal
structures of a DEXD/H-box protein in its open and closed cleft conformations.
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Selected figure(s)
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Figure 1.
Structure of human DDX19. A, overview of DDX19 with ADP bound
and the N-terminal flanking helix in the central cleft. The
Arg^429 side chain that acts as an arginine finger is presented
as sticks. B, schematic representation of the cleft-inserted
helix with the two conserved domains of the protein, shown in
the same view as in panel A. Residues that are conserved in
DDX25 are shown in blue. C, overview of the DDX19-RNA complex,
with Mg-ADPNP bound in the central cleft. The Arg^429 side chain
is presented as sticks. D, detail of the RNA binding site of the
DDX19-RNA complex. E, detail of the nucleotide binding site in
the open conformation, with the electron density (2F[obs] –
F[calc]) for ADP rendered at 1.5 σ. F, detail of the nucleotide
binding site in the RNA complex, with the electron density
(2F[obs] – F[calc]) for Mg-ADPNP rendered at 1.5 σ. In all
panels, the conserved domain-1 (yellow), the conserved domain-2
(red), and the N-terminal flanking sequence (green) are
indicated.
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Figure 2.
Role of the N-terminal flanking sequence in the regulation of
DDX19 ATPase activity. A, schematic diagram of the DDX19 protein
constructs used in this study (not drawn to scale). N-term
represents the N terminus. B, relative ATPase activities of
DDX19 protein constructs in the presence of between 0 and 0.5
mg/ml ssRNA.
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The above figures are
reprinted
from an Open Access publication published by the ASBMB:
J Biol Chem
(2009,
284,
10296-10300)
copyright 2009.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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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.
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Nature,
472,
238-242.
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PDB codes:
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D.Klostermeier
(2011).
Single-molecule FRET reveals nucleotide-driven conformational changes in molecular machines and their link to RNA unwinding and DNA supercoiling.
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Biochem Soc Trans,
39,
611-616.
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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.
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Biol Chem,
392,
357-369.
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PDB codes:
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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.
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Nucleic Acids Res,
39,
2260-2270.
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P.Linder,
and
E.Jankowsky
(2011).
From unwinding to clamping - the DEAD box RNA helicase family.
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Nat Rev Mol Cell Biol,
12,
505-516.
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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.
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J Mol Biol,
398,
429-443.
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M.Gu,
and
C.M.Rice
(2010).
Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism.
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Proc Natl Acad Sci U S A,
107,
521-528.
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PDB codes:
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M.Stewart
(2010).
Nuclear export of mRNA.
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Trends Biochem Sci,
35,
609-617.
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P.Schütz,
T.Karlberg,
S.van den Berg,
R.Collins,
L.Lehtiö,
M.Högbom,
L.Holmberg-Schiavone,
W.Tempel,
H.W.Park,
M.Hammarström,
M.Moche,
A.G.Thorsell,
and
H.Schüler
(2010).
Comparative structural analysis of human DEAD-box RNA helicases.
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PLoS One,
5,
0.
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PDB codes:
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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.
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Nucleic Acids Res,
38,
6219-6233.
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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.
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Nucleic Acids Res,
37,
4464-4471.
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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.
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Acta Crystallogr Sect F Struct Biol Cryst Commun,
65,
832-835.
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M.Del Campo,
and
A.M.Lambowitz
(2009).
Structure of the Yeast DEAD box protein Mss116p reveals two wedges that crimp RNA.
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Mol Cell,
35,
598-609.
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PDB codes:
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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.
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RNA,
15,
1993-2001.
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PDB codes:
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M.Hilbert,
A.R.Karow,
and
D.Klostermeier
(2009).
The mechanism of ATP-dependent RNA unwinding by DEAD box proteins.
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Biol Chem,
390,
1237-1250.
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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.
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Proc Natl Acad Sci U S A,
106,
16251-16256.
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PDB code:
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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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Links
