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PDBsum entry 1ueb
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RNA binding protein
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PDB id
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1ueb
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Crystal structure of elongation factor p from thermus thermophilus hb8.
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Authors
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K.Hanawa-Suetsugu,
S.Sekine,
H.Sakai,
C.Hori-Takemoto,
T.Terada,
S.Unzai,
J.R.Tame,
S.Kuramitsu,
M.Shirouzu,
S.Yokoyama.
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Ref.
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Proc Natl Acad Sci U S A, 2004,
101,
9595-9600.
[DOI no: ]
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PubMed id
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Abstract
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Translation elongation factor P (EF-P) stimulates ribosomal peptidyltransferase
activity. EF-P is conserved in bacteria and is essential for cell viability.
Eukarya and Archaea have an EF-P homologue, eukaryotic initiation factor 5A
(eIF-5A). In the present study, we determined the crystal structure of EF-P from
Thermus thermophilus HB8 at a 1.65-A resolution. EF-P consists of three
beta-barrel domains (I, II, and III), whereas eIF-5A has only two domains (N and
C domains). Domain I of EF-P is topologically the same as the N domain of
eIF-5A. On the other hand, EF-P domains II and III share the same topology as
that of the eIF-5A C domain, indicating that domains II and III arose by
duplication. Intriguingly, the N-terminal half of domain II and the C-terminal
half of domain III of EF-P have sequence homologies to the N- and C-terminal
halves, respectively, of the eIF-5A C domain. The three domains of EF-P are
arranged in an "L" shape, with 65- and 53-A-long arms at an angle of
95 degrees, which is reminiscent of tRNA. Furthermore, most of the EF-P protein
surface is negatively charged. Therefore, EF-P mimics the tRNA shape but uses
domain topologies different from those of the known tRNA-mimicry translation
factors. Domain I of EF-P has a conserved positive charge at its tip, like the
eIF-5A N domain.
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Figure 3.
Fig. 3. Structure comparison of EF-P with tRNA and
ribosome-binding proteins. (A and B) EF-P from T. thermophilus
(PDB ID code 1UEB [PDB]
). (C) tRNA^Phe from Saccharomyces cerevisiae (PDB ID code 1EVV
[PDB]
). (D) EF-G from T. thermophilus (PDB ID code 1EFG [PDB]
). (E) Ribosome recycling factor from E. coli (PDB code 1EK8 [PDB]
). (F) Release factor 2 from E. coli (PDB ID code 1GQE [PDB]
).
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Figure 5.
Fig. 5. Structure comparison of EF-P and eIF-5A. (A)
Superimposition of the ribbon diagrams of T. thermophilus EF-P
(blue) and M. jannaschii eIF-5A (yellow). (B) Amino acid
residues conserved in EF-Ps and eIF-5As color-coded on the
surface of T. thermophilus EF-P.
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