PDBsum entry 1e7z

RNA binding domain

PDB id: 1e7z

Contents

Protein chain

173 a.a. *

Metals

_HG ×2

Waters ×142

* Residue conservation analysis

PDB id:

1e7z

Name:

RNA binding domain

Title:

Crystal structure of the emap2/RNA binding domain of the p43 protein from human aminoacyl-tRNA synthetase complex

Structure:

Endothelial-monocyte activating polypeptide ii. Chain: a. Fragment: c-terminal domain/RNA binding domain residues 147-312. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.05Å R-factor: 0.221 R-free: 0.272

Authors:

S.Pasqualato,P.Kerjan,L.Renault,J.Menetrey,M.Mirande,J.Cherfils

Key ref:

L.Renault et al. (2001). Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry. EMBO J, 20, 570-578. PubMed id: 11157763 DOI: 10.1093/emboj/20.3.570

Date:

13-Sep-00 Release date: 27-Nov-00

Protein chain

Q12904  (AIMP1_HUMAN) -  Aminoacyl tRNA synthase complex-interacting multifunctional protein 1 from Homo sapiens

Seq: 312 a.a.

Struc: 173 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1093/emboj/20.3.570

EMBO J 20:570-578 (2001)

PubMed id: 11157763

Structure of the EMAPII domain of human aminoacyl-tRNA synthetase complex reveals evolutionary dimer mimicry.

L.Renault, P.Kerjan, S.Pasqualato, J.Ménétrey, J.C.Robinson, S.Kawaguchi, D.G.Vassylyev, S.Yokoyama, M.Mirande, J.Cherfils.

ABSTRACT

The EMAPII (endothelial monocyte-activating polypeptide II) domain is a tRNA-binding domain associated with several aminoacyl-tRNA synthetases, which becomes an independent domain with inflammatory cytokine activity upon apoptotic cleavage from the p43 component of the multisynthetase complex. It comprises a domain that is highly homologous to bacterial tRNA-binding proteins (Trbp), followed by an extra domain without homology to known proteins. Trbps, which may represent ancient tRNA chaperones, form dimers and bind one tRNA per dimer. In contrast, EMAPII domains are monomers. Here we report the crystal structure at 1.14 Angstroms of human EMAPII. The structure reveals that the Trbp-like domain, which forms an oligonucleotide-binding (OB) fold, is related by degenerate 2-fold symmetry to the extra-domain. The pseudo-axis coincides with the dyad axis of bacterial TtCsaA, a Trbp whose structure was solved recently. The interdomain interface in EMAPII mimics the intersubunit interface in TtCsaA, and may thus generate a novel OB-fold-based tRNA-binding site. The low sequence homology between the extra domain of EMAPII and either its own OB fold or that of Trbps suggests that dimer mimicry originated from convergent evolution rather than gene duplication.

Selected figure(s)

Figure 1.
Figure 1 Structure of EMAPII. (A) Overall view of human EMAPII/p43. The five -strands of the OB fold are in violet, the linker region in orange and the C-terminal domain in yellow. The His-tag in the C-terminus is shown as a dotted line. (B) Alignment of sequences of selected p43 (Hs, Homo sapiens; Dm, Drosophila melanogaster; Eo, Euplotes octocarinatus; At, Arabidopsis thaliana) and p43-related proteins (Sc, Saccharomyces cerevisiae; Os, Oriza sativa; Tp, Treponema pallidum; Ec, E.coli; Aa, A.aeolicus; Tt, T.thermophilus). Helices (rectangles) and strands (arrows) are coloured as in (A). Amino acids conserved in >50% of sequences are boxed in black. Hydrophobic residues at the domain interface are on a yellow background. The conserved motif in the C-terminal domain is highlighted in red.

Figure 2.
Figure 2 The internal pseudo-dyad in human EMAPII coincides with the 2-fold axis in bacterial CsaA. (A) Stereoview of EMAPII (in violet) superimposed onto itself (in orange), with superimposable regions shown as thick lines. The pseudo 2-fold axis is shown by an arrow. (B) The C-terminus domain of EMAPII (in yellow) is related by 2-fold symmetry to a subset of the OB fold (in dark violet). (C) Crystal structure of CsaA from T.thermophilus (Kawaguchi et al., 2001). A subset of the N-terminus of the symmetrical subunit (in yellow) matches the C-terminus domain of EMAPII. Orientations in (A), (B) and (C) are as in Figure 1A. (D) Structure-based sequence alignment of the C-terminal domain of EMAPII with its N-terminus domain and with the symmetry-related subunit of CsaA. Helices and strands are on a coloured background, with helices boxed. The C-domain of EMAPII is superimposable as a continuous peptide. Dots indicate residues of EMAPII (N-terminal domain) or CsaA (symmetry-related subunit) that superimpose with the C-terminus domain within a 2.5 Å cutoff; numbers indicate the length of non-superposable intervening sequences.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2001, 20, 570-578) copyright 2001.

Figures were selected by an automated process.