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PDBsum entry 1wrb
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Crystal structure of the n-terminal reca-like domain of djvlgb, a pranarian vasa-like RNA helicase
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Structure:
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Djvlgb. Chain: a, b. Fragment: n-terminal reca-like domain. Engineered: yes
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Source:
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Dugesia japonica. Organism_taxid: 6161. Other_details: e.Coli cell free system
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Resolution:
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2.40Å
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R-factor:
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0.241
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R-free:
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0.282
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Authors:
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K.Kurimoto,Y.Muto,N.Obayashi,T.Terada,M.Shirouzu,T.Yabuki,M.Aoki, E.Seki,T.Matsuda,T.Kigawa,H.Okumura,A.Tanaka,N.Shibata,M.Kashikawa, K.Agata,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)
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Key ref:
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K.Kurimoto
et al.
(2005).
Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein.
J Struct Biol,
150,
58-68.
PubMed id:
DOI:
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Date:
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14-Oct-04
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Release date:
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12-Apr-05
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PROCHECK
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Headers
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References
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O97032
(O97032_DUGJA) -
RNA helicase (Fragment) from Dugesia japonica
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Seq:
Struc:
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781 a.a.
232 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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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
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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 Struct Biol
150:58-68
(2005)
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PubMed id:
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Crystal structure of the N-terminal RecA-like domain of a DEAD-box RNA helicase, the Dugesia japonica vasa-like gene B protein.
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K.Kurimoto,
Y.Muto,
N.Obayashi,
T.Terada,
M.Shirouzu,
T.Yabuki,
M.Aoki,
E.Seki,
T.Matsuda,
T.Kigawa,
H.Okumura,
A.Tanaka,
N.Shibata,
M.Kashikawa,
K.Agata,
S.Yokoyama.
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ABSTRACT
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The Dugesia japonica vasa-like gene B (DjVLGB) protein is a DEAD-box RNA
helicase of a planarian, which is well known for its strong regenerative
capacity. DjVLGB shares sequence similarity to the Drosophila germ-line-specific
DEAD-box RNA helicase Vasa, and even higher similarity to its paralogue, mouse
PL10. In this study, we solved the crystal structure of the DjVLGB N-terminal
RecA-like domain. The overall fold and the structures of the putative ATPase
active site of the DjVLGB N-terminal RecA-like domain are similar to those of
the previously reported DEAD-box RNA helicase structures. In contrast, the
surface structure of the side opposite to the putative ATPase active site is
different from those of the other DEAD-box RNA helicases; the characteristic
hydrophobic pockets are formed with aromatic and proline residues. These
pocket-forming residues are conserved in the PL10-subfamily proteins, but less
conserved in the Vasa orthologues and not conserved in the DEAD-box RNA
helicases. Therefore, the structural features that we found are characteristic
of the PL10-subfamily proteins and might contribute to their biological roles in
germ-line development.
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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.Theissen,
A.R.Karow,
J.Köhler,
A.Gubaev,
and
D.Klostermeier
(2008).
Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase.
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Proc Natl Acad Sci U S A,
105,
548-553.
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T.Yabuki,
Y.Motoda,
K.Hanada,
E.Nunokawa,
M.Saito,
E.Seki,
M.Inoue,
T.Kigawa,
and
S.Yokoyama
(2007).
A robust two-step PCR method of template DNA production for high-throughput cell-free protein synthesis.
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J Struct Funct Genomics,
8,
173-191.
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K.Agata,
E.Nakajima,
N.Funayama,
N.Shibata,
Y.Saito,
and
Y.Umesono
(2006).
Two different evolutionary origins of stem cell systems and their molecular basis.
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Semin Cell Dev Biol,
17,
503-509.
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T.Hayashi,
M.Asami,
S.Higuchi,
N.Shibata,
and
K.Agata
(2006).
Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting.
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Dev Growth Differ,
48,
371-380.
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T.Sengoku,
O.Nureki,
A.Nakamura,
S.Kobayashi,
and
S.Yokoyama
(2006).
Structural basis for RNA unwinding by the DEAD-box protein Drosophila Vasa.
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Cell,
125,
287-300.
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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
code is
shown on the right.
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Links
