PDBsum entry 1ueb

RNA binding protein

PDB id: 1ueb

Contents

Protein chains

184 a.a. *

Waters ×407

* Residue conservation analysis

PDB id:

1ueb

Name:

RNA binding protein

Title:

Crystal structure of translation elongation factor p from thermus thermophilus hb8

Structure:

Elongation factor p. Chain: a, b. Synonym: ef-p, tt0860. Engineered: yes

Source:

Thermus thermophilus. Organism_taxid: 274. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.65Å R-factor: 0.213 R-free: 0.241

Authors:

K.Hanawa-Suetsugu,S.Sekine,H.Sakai,C.Hori-Takemoto,T.Terada, S.Kuramitsu,M.Shirouzu,S.Yokoyama,Riken Structural Genomics/proteomics Initiative (Rsgi)

Key ref:

K.Hanawa-Suetsugu et al. (2004). Crystal structure of elongation factor P from Thermus thermophilus HB8. Proc Natl Acad Sci U S A, 101, 9595-9600. PubMed id: 15210970 DOI: 10.1073/pnas.0308667101

Date:

09-May-03 Release date: 25-May-04

Protein chains

Q76G20  (EFP_THET8) -  Elongation factor P from Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)

Seq: 184 a.a.

Struc: 184 a.a.

DOI no: 10.1073/pnas.0308667101

Proc Natl Acad Sci U S A 101:9595-9600 (2004)

PubMed id: 15210970

Crystal structure of elongation factor P from Thermus thermophilus HB8.

K.Hanawa-Suetsugu, S.Sekine, H.Sakai, C.Hori-Takemoto, T.Terada, S.Unzai, J.R.Tame, S.Kuramitsu, M.Shirouzu, S.Yokoyama.

ABSTRACT

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.

Selected figure(s)

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] ).

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.

Figures were selected by an automated process.