PDBsum entry 1euj

Cytokine

PDB id: 1euj

Contents

Protein chains

164 a.a. *

Waters ×193

* Residue conservation analysis

PDB id:

1euj

Name:

Cytokine

Title:

A novel anti-tumor cytokine contains a RNA-binding motif present in aminoacyl-tRNA synthetases

Structure:

Endothelial monocyte activating polypeptide 2. Chain: a, b. Synonym: emap 2. Engineered: yes

Source:

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

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.208 R-free: 0.232

Authors:

Y.Kim,J.Shin,R.Li,C.Cheong,S.Kim

Key ref:

Y.Kim et al. (2000). A novel anti-tumor cytokine contains an RNA binding motif present in aminoacyl-tRNA synthetases. J Biol Chem, 275, 27062-27068. PubMed id: 10852899 DOI: 10.1074/jbc.C000216200

Date:

17-Apr-00 Release date: 06-Sep-00

Protein chains

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

Seq: 312 a.a.

Struc: 164 a.a.

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.C000216200

J Biol Chem 275:27062-27068 (2000)

PubMed id: 10852899

A novel anti-tumor cytokine contains an RNA binding motif present in aminoacyl-tRNA synthetases.

Y.Kim, J.Shin, R.Li, C.Cheong, K.Kim, S.Kim.

ABSTRACT

Endothelial monocyte-activating polypeptide II (EMAP II) is a novel pro-apoptotic cytokine that shares sequence homology with the C-terminal regions of several tRNA synthetases. Pro-EMAP II, the precursor of EMAP II, is associated with the multi-tRNA synthetase complex and facilitates aminoacylation activity. The structure of human EMAP II, solved at 1.8 A resolution, revealed the oligomer-binding fold for binding different tRNAs and a domain that is structurally homologous to other chemokines. The similar structures to the RNA binding motif of EMAP II was previously observed in the anticodon binding domain of yeast Asp-tRNA synthetase (AspRSSC) and the B2 domain of Thermus thermophilus Phe-tRNA synthetase. The RNA binding pattern of EMAP II is likely to be nonspecific, in contrast to the AspRSSC. The peptide sequence that is responsible for cytokine activity is located, for the most part, in the beta1 strand. It is divided into two regions by a neighboring loop.

Selected figure(s)

Figure 3.
Fig. 3. Comparison of RNA binding motifs in the OB folds of EMAP II and AspRSSC (23) structures. The orientations and residues are the same as described for Fig. 2A. The nomenclature of secondary structure elements follows the same convention as used in Figs. 1C and 2B. A, anticodon binding motif of AspRSSC. The 5 residues are shown to interact specifically with the three anticodon bases of Asp-tRNA by hydrogen bonds. Loop L5 is oriented so that it forms a valley to generate the binding pocket for the anticodon bases of Asp-tRNA. N represents the location of Ser-105 and C the location of Ser-198. B, RNA binding motif of EMAP II. The probable candidate residues, which may interact with tRNAs nonspecifically, are inferred from a comparison of the conserved residues in the EMAP II-like domains (4) with those involved in anticodon base interactions in the AspRSSC structure (23). The 5 hydrophilic residues are positioned in the smooth surface formed by loop L4, the strands 5i and 6i headed to the C terminus, whereas the residues of AspRSSC form a valley for the binding pocket of anticodon bases. N represents the location of Arg-8 and C the location of Pro-87.

Figure 4.
Fig. 4. Domain with cytokine activity. Stereo views of EMAP II are shown as C traces, truncated at residue 133 for a clear view. The view is in the same orientation as Fig. 3B. The domain, consisting of the residues 13-57, which is homologous to the chemokines, is shown in gray and consists of three strands ( 1- 3) and one short helix ( 1). The peptide sequence (residues 12-18) involved in chemotaxis of EMAP II is positioned at the beginning of this homologous domain. Three residues, Cys-15, Ile-17, and Thr-18, which were exposed to solvent, are shown by ball-and-stick symbols close to the end of strand 1. The other functional peptide sequence (residues 6-11) is located at the other side of a loop formed by residues 99-102. The hydrophobic residues Val-6, Leu-8, and Leu-11 form a shallow hydrophobic pocket with Phe-107 and Leu-132. N represents the location of Pro-3 and C the location of His-133. The C s of residues 12, 99, and 102 are shown as black circles.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 27062-27068) copyright 2000.

Figures were selected by an automated process.